From a1297082e2df74e672512334238143542ad323ce Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Tue, 19 Nov 2024 14:57:18 +0100 Subject: [PATCH 01/15] Crossref Enhancements: -Accurate Review Type Assignment: Resolved an issue identified in ticket https://support.openaire.eu/issues/9525#note-13. When a relationship of "is-review-of" is detected, the publication type is now correctly set to "Review." -Enhanced Author Affiliation Data: Implemented Miriam's suggestion by including a new field, "RawAffiliationString," in each author entry. This additional data provides a more granular level of detail regarding author affiliations, potentially improving discoverability and research analysis. --- .../collection/crossref/Crossref2Oaf.scala | 67 ++--- .../collection/crossref/affiliationTest.json | 232 ++++++++++++++++++ .../crossref/CrossrefMappingTest.scala | 12 +- 3 files changed, 265 insertions(+), 46 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala index e7d68920b8..e15312e43a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala @@ -37,7 +37,7 @@ case class mappingAuthor( family: Option[String], sequence: Option[String], ORCID: Option[String], - affiliation: Option[mappingAffiliation] + affiliation: Option[List[mappingAffiliation]] ) {} case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {} @@ -457,15 +457,14 @@ case object Crossref2Oaf { } //Mapping Author - val authorList: List[mappingAuthor] = - (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined) + val authorList: List[mappingAuthor] = (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined) val sorted_list = authorList.sortWith((a: mappingAuthor, b: mappingAuthor) => a.sequence.isDefined && a.sequence.get.equalsIgnoreCase("first") ) result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) => - generateAuhtor(a.given.orNull, a.family.get, a.ORCID.orNull, index) + generateAuthor(a.given.orNull, a.family.get, a.ORCID.orNull, index, a.affiliation) }.asJava) // Mapping instance @@ -504,18 +503,6 @@ case object Crossref2Oaf { ) } - val is_review = json \ "relation" \ "is-review-of" \ "id" - - if (is_review != JNothing) { - instance.setInstancetype( - OafMapperUtils.qualifier( - "0015", - "peerReviewed", - ModelConstants.DNET_REVIEW_LEVELS, - ModelConstants.DNET_REVIEW_LEVELS - ) - ) - } if (doi.startsWith("10.3410") || doi.startsWith("10.12703")) instance.setHostedby( @@ -569,17 +556,24 @@ case object Crossref2Oaf { result } + + def generateIdentifier(oaf: Result, doi: String): String = { val id = DHPUtils.md5(doi.toLowerCase) s"50|doiboost____|$id" } - def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = { + private def generateAuthor(given: String, family: String, orcid: String, index: Int, affiliation: Option[List[mappingAffiliation]]): Author = { val a = new Author a.setName(given) a.setSurname(family) a.setFullname(s"$given $family") a.setRank(index + 1) + + // Adding Raw affiliation if it's defined + if (affiliation.isDefined) { + a.setRawAffiliationString(affiliation.get.map(a => a.name).asJava) + } if (StringUtils.isNotBlank(orcid)) a.setPid( List( @@ -705,11 +699,21 @@ case object Crossref2Oaf { val objectType = (json \ "type").extractOrElse[String](null) if (objectType == null) return resultList - val typology = getTypeQualifier(objectType, vocabularies) + + + // If the item has a relations is-review-of, then we force it to a peer-review + val is_review = json \ "relation" \ "is-review-of" \ "id" + var force_to_review = false + if (is_review != JNothing) { + force_to_review = true + } + + val typology = getTypeQualifier(if (force_to_review) "peer-review" else objectType, vocabularies) if (typology == null) return List() + val result = generateItemFromType(typology._2) if (result == null) return List() @@ -757,33 +761,6 @@ case object Crossref2Oaf { else resultList } - - // if (uw != null) { -// result.getCollectedfrom.add(createUnpayWallCollectedFrom()) -// val i: Instance = new Instance() -// i.setCollectedfrom(createUnpayWallCollectedFrom()) -// if (uw.best_oa_location != null) { -// -// i.setUrl(List(uw.best_oa_location.url).asJava) -// if (uw.best_oa_location.license.isDefined) { -// i.setLicense(field[String](uw.best_oa_location.license.get, null)) -// } -// -// val colour = get_unpaywall_color(uw.oa_status) -// if (colour.isDefined) { -// val a = new AccessRight -// a.setClassid(ModelConstants.ACCESS_RIGHT_OPEN) -// a.setClassname(ModelConstants.ACCESS_RIGHT_OPEN) -// a.setSchemeid(ModelConstants.DNET_ACCESS_MODES) -// a.setSchemename(ModelConstants.DNET_ACCESS_MODES) -// a.setOpenAccessRoute(colour.get) -// i.setAccessright(a) -// } -// i.setPid(result.getPid) -// result.getInstance().add(i) -// } -// } - } private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = { diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json new file mode 100644 index 0000000000..201138e45b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json @@ -0,0 +1,232 @@ +{ + "indexed": { + "date-parts": [ + [ + 2022, + 4, + 3 + ] + ], + "date-time": "2022-04-03T01:45:59Z", + "timestamp": 1648950359167 + }, + "reference-count": 0, + "publisher": "American Society of Clinical Oncology (ASCO)", + "issue": "18_suppl", + "content-domain": { + "domain": [], + "crossmark-restriction": false + }, + "short-container-title": [ + "JCO" + ], + "published-print": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + }, + "abstract": " 3507 Purpose: To detect IGF-1R on circulating tumor cells (CTCs) as a biomarker in the clinical development of a monoclonal human antibody, CP-751,871, targeting IGF-1R. Experimental Design: An automated sample preparation and analysis system for enumerating CTCs (Celltracks) was adapted for detecting IGF-1R positive CTCs with a diagnostic antibody targeting a different IGF-1R epitope to CP-751,871. This assay was utilized in three phase I trials of CP-751,871 as a single agent or with chemotherapy and was validated using cell lines and blood samples from healthy volunteers and patients with metastatic carcinoma. Results: There was no interference between the analytical and therapeutic antibodies. CP-751,871 was well tolerated as a single agent, and in combination with docetaxel or carboplatin and paclitaxel, at doses ranging from 0.05 mg/kg to 20 mg/kg. Eighty patients were enrolled on phase 1 studies of CP-751,871, with 47 (59%) patients having CTCs detected during the study. Prior to treatment 26 patients (33%) had CTCs, with 23 having detectable IGF-1R positive CTCs. CP-751,871 alone, and CP-751,871 with cytotoxic chemotherapy, decreased CTCs and IGF-1R positive CTCs; these increased towards the end of the 21-day cycle in some patients, falling again with retreatment. CTCs were commonest in advanced hormone refractory prostate cancer (11/20). Detectable IGF-1R expression on CTCs before treatment with CP-751,871 and docetaxel was associated with a higher frequency of PSA decline by more than 50% (6/10 vs 2/8 patients). A relationship was observed between sustained falls in CTCs counts and PSA declines by more than 50%. Conclusions: IGF-1R expression is detectable by immunofluorescence on CTCs. These data support the further evaluation of CTCs in pharmacodynamic studies and patient selection, particularly in advanced prostate cancer. No significant financial relationships to disclose. ", + "DOI": "10.1200/jco.2007.25.18_suppl.3507", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2020, + 3, + 6 + ] + ], + "date-time": "2020-03-06T20:50:42Z", + "timestamp": 1583527842000 + }, + "page": "3507-3507", + "source": "Crossref", + "is-referenced-by-count": 0, + "title": [ + "Circulating tumor cells expressing the insulin growth factor-1 receptor (IGF-1R): Method of detection, incidence and potential applications" + ], + "prefix": "10.1200", + "volume": "25", + "author": [ + { + "given": "J. S.", + "family": "de Bono", + "sequence": "first", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "A.", + "family": "Adjei", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "G.", + "family": "Attard", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "M.", + "family": "Pollak", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "P.", + "family": "Fong", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "P.", + "family": "Haluska", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "L.", + "family": "Roberts", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "D.", + "family": "Chainese", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "L.", + "family": "Terstappen", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + }, + { + "given": "A.", + "family": "Gualberto", + "sequence": "additional", + "affiliation": [ + { + "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA" + } + ] + } + ], + "member": "233", + "container-title": [ + "Journal of Clinical Oncology" + ], + "original-title": [], + "language": "en", + "deposited": { + "date-parts": [ + [ + 2020, + 3, + 6 + ] + ], + "date-time": "2020-03-06T20:51:03Z", + "timestamp": 1583527863000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "http://ascopubs.org/doi/10.1200/jco.2007.25.18_suppl.3507" + } + }, + "subtitle": [], + "short-title": [], + "issued": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + }, + "references-count": 0, + "journal-issue": { + "issue": "18_suppl", + "published-print": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + } + }, + "alternative-id": [ + "10.1200/jco.2007.25.18_suppl.3507" + ], + "URL": "http://dx.doi.org/10.1200/jco.2007.25.18_suppl.3507", + "relation": {}, + "ISSN": [ + "0732-183X", + "1527-7755" + ], + "issn-type": [ + { + "value": "0732-183X", + "type": "print" + }, + { + "value": "1527-7755", + "type": "electronic" + } + ], + "subject": [], + "published": { + "date-parts": [ + [ + 2007, + 6, + 20 + ] + ] + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala index c3ea884eb3..f6f71ca669 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala @@ -25,8 +25,18 @@ class CrossrefMappingTest extends AbstractVocabularyTest { val input = IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8") - println(Crossref2Oaf.convert(input, vocabularies, TransformationType.All)) + Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => { + println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(record)) + }) } + + @Test + def mappingAffiliation(): Unit = { + val input = + IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8") + val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult) + println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head)) + } } From 496007188a720b18ce8301b6050c6e0b924522d1 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 20 Nov 2024 09:50:09 +0100 Subject: [PATCH 02/15] Added assertion on CrossrefMappingTest --- .../crossref/CrossrefMappingTest.scala | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala index f6f71ca669..12ca14ba14 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala @@ -3,12 +3,15 @@ package eu.dnetlib.dhp.collection.crossref import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.collection.crossref.Crossref2Oaf.TransformationType +import eu.dnetlib.dhp.schema.oaf.Publication import org.apache.commons.io.IOUtils -import org.junit.jupiter.api.{BeforeEach, Test} +import org.junit.jupiter.api.{Assertions, BeforeEach, Test} import org.junit.jupiter.api.extension.ExtendWith import org.mockito.junit.jupiter.MockitoExtension import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters.asScalaBufferConverter + @ExtendWith(Array(classOf[MockitoExtension])) class CrossrefMappingTest extends AbstractVocabularyTest { @@ -26,7 +29,7 @@ class CrossrefMappingTest extends AbstractVocabularyTest { IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8") Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => { - println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(record)) + Assertions.assertNotNull(record) }) } @@ -37,6 +40,16 @@ class CrossrefMappingTest extends AbstractVocabularyTest { val input = IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8") val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult) + data.foreach(record => { + Assertions.assertNotNull(record) + Assertions.assertTrue(record.isInstanceOf[Publication]) + val publication = record.asInstanceOf[Publication] + publication.getAuthor.asScala.foreach(author => { + Assertions.assertNotNull(author.getRawAffiliationString) + Assertions.assertTrue(author.getRawAffiliationString.size()>0) + + }) + }) println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head)) } } From e5b04e61ff8f7f7b1d80f607e0fcb4da7c7c9f37 Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Thu, 21 Nov 2024 10:20:12 +0100 Subject: [PATCH 03/15] [CommunityPatents] extends the community propagation considering also the results of type patents linked with a isrelatedto semantcis --- .../main/java/eu/dnetlib/dhp/api/Utils.java | 2 +- .../PrepareResultCommunitySetStep1.java | 51 ++++++++++++++++--- .../PrepareResultCommunitySetStep2.java | 18 ++----- 3 files changed, 49 insertions(+), 22 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java index 6079da3656..1e39d99c3d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -171,7 +171,7 @@ public class Utils implements Serializable { public static List getCommunityIdList(String baseURL) throws IOException { return getValidCommunities(baseURL) .stream() - .map(community -> community.getId()) + .map(CommunityModel::getId) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index aede9ef05b..ff496bb878 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -3,11 +3,14 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static java.lang.String.join; import java.io.IOException; import java.util.Arrays; +import java.util.Collections; import java.util.List; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.sql.*; @@ -45,7 +48,7 @@ public class PrepareResultCommunitySetStep1 { /** * a dataset for example could be linked to more than one publication. For each publication linked to that dataset - * the previous query will produce a row: targetId set of community context the target could possibly inherit with + * the previous query will produce a row: targetId, set of community context the target could possibly inherit. With * the following query there will be a single row for each result linked to more than one result of the result type * currently being used */ @@ -56,6 +59,16 @@ public class PrepareResultCommunitySetStep1 { + "where length(co) > 0 " + "group by resultId"; + private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target resultId, community_context " + + "from (select id, collect_set(co.id) community_context " + + " from result " + + " lateral view explode (context) c as co " + + " where datainfo.deletedbyinference = false %s " + + " and array_contains(instance.instancetype.classname, 'Patent') group by id) p " + + " JOIN " + + " (select source, target from relation " + + " where datainfo.deletedbyinference = false %s ) r ON p.id = r.source"; + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -82,15 +95,20 @@ public class PrepareResultCommunitySetStep1 { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final List allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";")); + final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)); + log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}", baseURL); - final List communityIdList = getCommunityList(baseURL); - log.info("communityIdList: {}", new Gson().toJson(communityIdList)); + final String communityIdList = join(",", getCommunityList(baseURL).stream() + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)); + log.info("communityIdList: {}", new Gson().toJson(communityIdList)); final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase(); log.info("resultType: {}", resultType); @@ -118,10 +136,10 @@ public class PrepareResultCommunitySetStep1 { SparkSession spark, String inputPath, String outputPath, - List allowedsemrel, + String allowedsemrel, Class resultClazz, String resultType, - List communityIdList) { + String communityIdList) { final String inputResultPath = inputPath + "/" + resultType; log.info("Reading Graph table from: {}", inputResultPath); @@ -141,8 +159,15 @@ public class PrepareResultCommunitySetStep1 { String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - getConstraintList(" lower(co.id) = '", communityIdList), - getConstraintList(" lower(relClass) = '", allowedsemrel)); + " lower(co.id) IN " + communityIdList, + " AND lower(relClass) IN " + allowedsemrel); + + String resultContextQueryIsRelatedTo = String + .format( + RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO, + " AND lower(co.id) IN " + communityIdList, + "AND lower(relClass) = '"+ + ModelConstants.IS_RELATED_TO.toLowerCase() + "'"); Dataset result_context = spark.sql(resultContextQuery); result_context.createOrReplaceTempView("result_context"); @@ -154,6 +179,16 @@ public class PrepareResultCommunitySetStep1 { .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputResultPath); + + result_context = spark.sql(resultContextQueryIsRelatedTo); + result_context.createOrReplaceTempView("result_context"); + spark + .sql(RESULT_COMMUNITY_LIST_QUERY) + .as(Encoders.bean(ResultCommunityList.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Append) + .json(outputResultPath); } public static List getCommunityList(final String baseURL) throws IOException { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java index a53d3dfe32..9bebc36e58 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.ArrayList; import java.util.HashSet; import java.util.Set; @@ -76,22 +77,13 @@ public class PrepareResultCommunitySetStep2 { if (b == null) { return a; } - Set community_set = new HashSet<>(); - a.getCommunityList().stream().forEach(aa -> community_set.add(aa)); - b - .getCommunityList() - .stream() - .forEach( - aa -> { - if (!community_set.contains(aa)) { - a.getCommunityList().add(aa); - community_set.add(aa); - } - }); + Set community_set = new HashSet<>(a.getCommunityList()); + community_set.addAll(b.getCommunityList()); + a.setCommunityList(new ArrayList<>(community_set)); return a; }) .map(Tuple2::_2) - .map(r -> OBJECT_MAPPER.writeValueAsString(r)) + .map(OBJECT_MAPPER::writeValueAsString) .saveAsTextFile(outputPath, GzipCodec.class); } From 821700299a31e5201f616fd4235dcd599018d19b Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Fri, 22 Nov 2024 17:21:58 +0100 Subject: [PATCH 04/15] [patents] added test and resources --- .../PrepareResultCommunitySetStep1.java | 93 +++++++++++-------- .../ResultToCommunityJobTest.java | 55 +++++++++++ .../graph/publication/part-00000.json | 13 +++ .../graph/relation/part-00000.json | 24 +++++ 4 files changed, 147 insertions(+), 38 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/relation/part-00000.json diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index ff496bb878..8f23a4cfdd 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -37,7 +37,8 @@ public class PrepareResultCommunitySetStep1 { * relation */ // TODO - private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context " + private static final String RESULT_CONTEXT_QUERY_TEMPLATE = + "select target resultId, community_context " + "from (select id, collect_set(co.id) community_context " + " from result " + " lateral view explode (context) c as co " @@ -59,15 +60,26 @@ public class PrepareResultCommunitySetStep1 { + "where length(co) > 0 " + "group by resultId"; - private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target resultId, community_context " - + "from (select id, collect_set(co.id) community_context " - + " from result " - + " lateral view explode (context) c as co " - + " where datainfo.deletedbyinference = false %s " - + " and array_contains(instance.instancetype.classname, 'Patent') group by id) p " - + " JOIN " - + " (select source, target from relation " - + " where datainfo.deletedbyinference = false %s ) r ON p.id = r.source"; + private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = + "select target as resultId, community_context " + + "from resultWithContext rwc " + + "join relatedToRelations r " + + "join patents p " + + "on rwc.id = r.source and r.target = p.id"; + + private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context \n" + + " from result " + + " lateral view explode (context) c as co " + + " where datainfo.deletedbyinference = false AND lower(co.id) IN %s" + + " group by id"; + + private static final String RESULT_PATENT = "select id " + + " from result " + + " where array_contains(instance.instancetype.classname, 'Patent')"; + + private static final String IS_RELATED_TO_RELATIONS = "select source, target " + + " from relation " + + " where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false"; public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -95,20 +107,18 @@ public class PrepareResultCommunitySetStep1 { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) - .map(value -> "'" + value.toLowerCase() + "'") - .toArray(String[]::new)); - - log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); + final String allowedsemrel ="(" + join(",", + Arrays.asList(parser.get("allowedsemrels").split(";")).stream().map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)) + ")"; + log.info("allowedSemRel: {}", allowedsemrel); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}", baseURL); - final String communityIdList = join(",", getCommunityList(baseURL).stream() + final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream() .map(value -> "'" + value.toLowerCase() + "'") - .toArray(String[]::new)); + .toArray(String[]::new)) + ")"; - log.info("communityIdList: {}", new Gson().toJson(communityIdList)); final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase(); log.info("resultType: {}", resultType); @@ -156,32 +166,38 @@ public class PrepareResultCommunitySetStep1 { final String outputResultPath = outputPath + "/" + resultType; log.info("writing output results to: {}", outputResultPath); + String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - " lower(co.id) IN " + communityIdList, - " AND lower(relClass) IN " + allowedsemrel); - - String resultContextQueryIsRelatedTo = String - .format( - RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO, - " AND lower(co.id) IN " + communityIdList, - "AND lower(relClass) = '"+ - ModelConstants.IS_RELATED_TO.toLowerCase() + "'"); - + "AND lower(co.id) IN " + communityIdList, + "AND lower(relClass) IN " + allowedsemrel); Dataset result_context = spark.sql(resultContextQuery); + //result_context.createOrReplaceTempView("result_context"); + +// spark +// .sql(RESULT_COMMUNITY_LIST_QUERY) +// .as(Encoders.bean(ResultCommunityList.class)) +// .write() +// .option("compression", "gzip") +// .mode(SaveMode.Overwrite) +// .json(outputResultPath); + + Dataset rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList)); + Dataset patents = spark.sql(RESULT_PATENT); + Dataset relatedToRelations = spark.sql(IS_RELATED_TO_RELATIONS); + + rwc.createOrReplaceTempView("resultWithContext"); + + patents.createOrReplaceTempView("patents"); + + relatedToRelations.createOrReplaceTempView("relatedTorelations"); + + + result_context = result_context.unionAll( spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO)); + result_context.createOrReplaceTempView("result_context"); - spark - .sql(RESULT_COMMUNITY_LIST_QUERY) - .as(Encoders.bean(ResultCommunityList.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputResultPath); - - result_context = spark.sql(resultContextQueryIsRelatedTo); - result_context.createOrReplaceTempView("result_context"); spark .sql(RESULT_COMMUNITY_LIST_QUERY) .as(Encoders.bean(ResultCommunityList.class)) @@ -189,6 +205,7 @@ public class PrepareResultCommunitySetStep1 { .option("compression", "gzip") .mode(SaveMode.Append) .json(outputResultPath); + } public static List getCommunityList(final String baseURL) throws IOException { diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index 0d5b12c808..4361b6f392 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java @@ -6,8 +6,11 @@ import static org.apache.spark.sql.functions.desc; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.ArrayList; import java.util.List; +import java.util.stream.Collectors; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -25,6 +28,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Dataset; +import scala.collection.Seq; public class ResultToCommunityJobTest { @@ -271,4 +275,55 @@ public class ResultToCommunityJobTest { .get(0) .getString(0)); } + + @Test + public void prepareStep1Test() throws Exception { + /* + + + final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)); + + log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); + + final String baseURL = parser.get("baseURL"); + log.info("baseURL: {}", baseURL); + */ + PrepareResultCommunitySetStep1 + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass() + .getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph") + .getPath(), + "-hive_metastore_uris", "", + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", workingDir.toString() + "/preparedInfo", + "-allowedsemrels","issupplementto;issupplementedby", + "-baseURL","https://dev-openaire.d4science.org/openaire/community/" + }); + + + org.apache.spark.sql.Dataset resultCommunityList = spark.read().schema(Encoders.bean(ResultCommunityList.class).schema()) + .json(workingDir.toString() + "/preparedInfo/publication") + .as(Encoders.bean(ResultCommunityList.class)); + + Assertions.assertEquals(2, resultCommunityList.count()); + Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count()); + Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count()); + + ArrayList communities = resultCommunityList + .filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'") + .first().getCommunityList(); + Assertions.assertEquals(2, communities.size()); + Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid))); + Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid))); + + communities = resultCommunityList + .filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'") + .first().getCommunityList(); + Assertions.assertEquals(1, communities.size()); + Assertions.assertEquals("dh-ch", communities.get(0)); + } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json new file mode 100644 index 0000000000..7957bcfd50 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json @@ -0,0 +1,13 @@ +{"author":[{"fullname":"Tanouayi, Gnon","name":"Gnon","pid":[],"rank":1,"surname":"Tanouayi"},{"fullname":"GNANDI, Kissao","name":"Kissao","pid":[],"rank":2,"surname":"Gnandi"},{"fullname":"Ouro-Sama, Kamilou","name":"Kamilou","pid":[],"rank":3,"surname":"Ouro-Sama"},{"fullname":"Ahoudi, Housséni","name":"Housséni","pid":[],"rank":4,"surname":"Ahoudi"},{"fullname":"Solitoke, Hodabalo Dhéoulaba","name":"Hodabalo Dhéoulaba","pid":[],"rank":5,"surname":"Solitoke"},{"fullname":"Badassan, Tchaa Esso-Essinam","name":"Tchaa Esso-Essinam","pid":[],"rank":6,"surname":"Badassan"},{"fullname":"Nyametso, A. Yawovi","name":"A. Yawovi","pid":[],"rank":7,"surname":"Nyametso"},{"fullname":"Agbéko, Aduayi-Akué Adoté","name":"Aduayi-Akué Adoté","pid":[],"rank":8,"surname":"Agbéko"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|eurocrisdris::fe4903425d9040f680d8610d9079ea14","value":"Episciences"}],"context":[],"contributor":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Importer of dst articles previously hosted by inist Eid system account"}],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2017-05-01"},"dateofcollection":"2022-03-01T00:17:08.896Z","dateoftransformation":"2022-03-01T02:57:50.566Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"This study is a contribution to the development of adsorption techniques for the removal of fluoride in natural waters. The work is carried out on a laboratory scale using local geo-materials sorbents, on the one hand the residues from the treatment of natural phosphorite of Hahotoé-Kpogamé and on the other hand the attapulgite clay mineral from the costal basin of Togo. The work carried out concerns the adsorption of fluoride on those sorbents. The following parameters are batch tested on synthetic fluoride solutions: time, solution pH, geo-material dose and fluoride concentration. The fluoride is analyzed by absorption spectrometry. The adsorption yields on the phosphorite treatment residues for aqueous fluoride solutions at an initial concentration of 10 mg/L and an adsorbent concentration of 10 g/L are 49 % at pH 6.5 and 66 % at pH 4.0. In the same experimental conditions, the yields on clay minerals are 28.2 % and 36.3 %. These yields are logically improved by increasing the adsorbent dosage (from 2 to 30 g/L). Additional tests are carried out on natural water at an initial fluoride concentration of 3.76 mg/L."},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Cette étude est une contribution au développement de techniques d’adsorption pour l’élimination du fluor dans les eaux naturelles. Les travaux ont été réalisés à l’échelle du laboratoire en utilisant comme sorbants des géo-matériaux locaux, d’une part les résidus du traitement des phosphates naturels de Hahotoé-Kpogamé et d’autre part l’argilite feuilletée du bassin sédimentaire côtier du Togo. Les travaux réalisés concernent l’adsorption du fluor sur les sorbants considérés. Les paramètres suivants ont été testés en batch sur des solutions synthétiques de fluor : le temps, le pH de la solution, la dose du géo-matériau et la concentration du fluor. Le fluor a été dosé par spectromètrie d’absorption. Les rendements d’adsorption sur les résidus de traitement des phosphates pour des solutions aqueuses de fluor à concentration initiale de 10 mg/L et une concentration en adsorbant de 10 g/L ont été de 49 % à pH 6,5 et 66 % à pH de 4,0. Dans les mêmes conditions expérimentales, les rendements sur les argilites ont été de 28,2 % et 36,3 %. Ces rendements ont logiquement été améliorés en augmentant le dosage en adsorbant (de 2 à 30 g/L). Des essais complémentaires ont été réalisés sur une eau naturelle à une concentration initiale en fluor de 3,76 mg/L."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"Digital Object 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Hydrolysates of lignocellulosic biomass, used as substrates for the sustainable production of fuels and chemicals often contain high amounts of phenolic compounds inhibiting the production microbiota. Quantification of these inhibitor compounds may help to understand possible difficulties in bioprocessing and further the development of more efficient, robust and tolerable processes. A separation method based on capillary electrophoresis with UV detection was developed for the simultaneous quantification of 10 phenolic compounds that may have inhibitor properties. Intraday relative standard deviations were less than 0.7% for migration times and between 2.6% and 6.4% for peak areas. Interday relative standard deviations were less than 3.0% for migration times and between 5.0% and 7.2% for peak areas. The method was applied to demonstrate that Saccharomyces cerevisiae was able to decrease the concentrations of vanillin, coniferyl aldehyde, syringaldehyde, acetoguaiacone and cinnamic acid during the cultivation, whereas the concentrations of phenols increased.

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Ex situ analyses of the tiles were performed by secondary ion mass spectrometry.
The peaks of 13C were detected below the bottom inner strike point and at the horizontal tile at the outer lower divertor. It was detected ∼21% of the total puffed 13C amount.
The deposition rate for carbon by plasma was also calculated in long term experiment. 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, R , Vanttaja , I , Haapamäki , P & Kujanpää , V 1994 , ' Liimauksen ja puristusliittämisen yhdistämisellä lisää lujuutta, jäykkyyttä ja tiiveyttä ' , Ohutlevyuutiset , no. 2 , pp. 17-19 ."}],"subject":[],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Liimauksen ja puristusliittämisen yhdistämisellä lisää lujuutta, jäykkyyttä ja tiiveyttä"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/relation/part-00000.json 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+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false} \ No newline at end of file From 189a7c255a52127f79db59d7cde171f216d76152 Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Mon, 25 Nov 2024 16:52:13 +0100 Subject: [PATCH 05/15] [patents] added test and resources --- .../PrepareResultCommunitySetStep1.java | 11 ----------- .../ResultToCommunityJobTest.java | 2 ++ 2 files changed, 2 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index 8f23a4cfdd..5af2bf4812 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -173,24 +173,13 @@ public class PrepareResultCommunitySetStep1 { "AND lower(co.id) IN " + communityIdList, "AND lower(relClass) IN " + allowedsemrel); Dataset result_context = spark.sql(resultContextQuery); - //result_context.createOrReplaceTempView("result_context"); - -// spark -// .sql(RESULT_COMMUNITY_LIST_QUERY) -// .as(Encoders.bean(ResultCommunityList.class)) -// .write() -// .option("compression", "gzip") -// .mode(SaveMode.Overwrite) -// .json(outputResultPath); Dataset rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList)); Dataset patents = spark.sql(RESULT_PATENT); Dataset relatedToRelations = spark.sql(IS_RELATED_TO_RELATIONS); rwc.createOrReplaceTempView("resultWithContext"); - patents.createOrReplaceTempView("patents"); - relatedToRelations.createOrReplaceTempView("relatedTorelations"); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index 4361b6f392..c1fcff4d99 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java @@ -326,4 +326,6 @@ public class ResultToCommunityJobTest { Assertions.assertEquals(1, communities.size()); Assertions.assertEquals("dh-ch", communities.get(0)); } + + } From 32e2a8b34053dc8162bf20bb91c977d544d05b94 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 4 Dec 2024 13:36:21 +0100 Subject: [PATCH 06/15] implemented zenodo dump collector plugin --- .../CollectZenodoDumpCollectorPlugin.java | 96 ++++++++++++++++++ .../plugin/zenodo/ZenodoTarIterator.java | 59 +++++++++++ .../zenodo/ZenodoPluginCollectionTest.java | 35 +++++++ .../dhp/collection/zenodo/zenodo.tar.gz | Bin 0 -> 7412 bytes 4 files changed, 190 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java new file mode 100644 index 0000000000..3ea29a9b03 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java @@ -0,0 +1,96 @@ + +package eu.dnetlib.dhp.collection.plugin.zenodo; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +import java.io.IOException; +import java.io.InputStream; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.http.client.config.RequestConfig; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClientBuilder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; + +public class CollectZenodoDumpCollectorPlugin implements CollectorPlugin { + + final private Logger log = LoggerFactory.getLogger(getClass()); + + private void downloadItem(final String name, final String itemURL, final String basePath, + final FileSystem fileSystem) { + try { + final Path hdfsWritePath = new Path(String.format("%s/%s", basePath, name)); + final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true); + final HttpGet request = new HttpGet(itemURL); + final int timeout = 60; // seconds + final RequestConfig config = RequestConfig + .custom() + .setConnectTimeout(timeout * 1000) + .setConnectionRequestTimeout(timeout * 1000) + .setSocketTimeout(timeout * 1000) + .build(); + log.info("Downloading url {} into {}", itemURL, hdfsWritePath.getName()); + try (CloseableHttpClient client = HttpClientBuilder.create().setDefaultRequestConfig(config).build(); + CloseableHttpResponse response = client.execute(request)) { + int responseCode = response.getStatusLine().getStatusCode(); + log.info("Response code is {}", responseCode); + if (responseCode >= 200 && responseCode < 400) { + IOUtils.copy(response.getEntity().getContent(), fsDataOutputStream); + } + } catch (Throwable eu) { + throw new RuntimeException(eu); + } + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + @Override + public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { + try { + final String zenodoURL = api.getBaseUrl(); + final String hdfsURI = api.getParams().get("hdfsURI"); + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(hdfsURI)); + downloadItem("zenodoDump.tar.gz", zenodoURL, "/tmp", fileSystem); + CompressionCodecFactory factory = new CompressionCodecFactory(fileSystem.getConf()); + + Path sourcePath = new Path("/tmp/zenodoDump.tar.gz"); + CompressionCodec codec = factory.getCodec(sourcePath); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fileSystem.open(sourcePath)); + return iterateTar(gzipInputStream); + + } catch (IOException e) { + throw new CollectorException(e); + } finally { + log.info("Closing gzip stream"); + org.apache.hadoop.io.IOUtils.closeStream(gzipInputStream); + } + } catch (Exception e) { + throw new CollectorException(e); + } + } + + private Stream iterateTar(InputStream gzipInputStream) throws Exception { + + Iterable iterable = () -> new ZenodoTarIterator(gzipInputStream); + return StreamSupport.stream(iterable.spliterator(), false); + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java new file mode 100644 index 0000000000..8e627683e6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java @@ -0,0 +1,59 @@ + +package eu.dnetlib.dhp.collection.plugin.zenodo; + +import java.io.Closeable; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.Iterator; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.io.IOUtils; + +public class ZenodoTarIterator implements Iterator, Closeable { + + private final InputStream gzipInputStream; + private final StringBuilder currentItem = new StringBuilder(); + private TarArchiveInputStream tais; + private boolean hasNext; + + public ZenodoTarIterator(InputStream gzipInputStream) { + this.gzipInputStream = gzipInputStream; + tais = new TarArchiveInputStream(gzipInputStream); + hasNext = getNextItem(); + } + + private boolean getNextItem() { + try { + TarArchiveEntry entry; + while ((entry = tais.getNextTarEntry()) != null) { + if (entry.isFile()) { + currentItem.setLength(0); + currentItem.append(IOUtils.toString(new InputStreamReader(tais))); + return true; + } + } + return false; + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + @Override + public boolean hasNext() { + return hasNext; + } + + @Override + public String next() { + final String data = currentItem.toString(); + hasNext = getNextItem(); + return data; + } + + @Override + public void close() throws IOException { + gzipInputStream.close(); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java new file mode 100644 index 0000000000..9b5cf1850f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.collection.plugin.zenodo; + +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import java.util.zip.GZIPInputStream; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.common.collection.CollectorException; + +public class ZenodoPluginCollectionTest { + + @Test + public void testZenodoIterator() throws Exception { + + final GZIPInputStream gis = new GZIPInputStream( + getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz")); + try (ZenodoTarIterator it = new ZenodoTarIterator(gis)) { + Assertions.assertTrue(it.hasNext()); + int i = 0; + while (it.hasNext()) { + Assertions.assertNotNull(it.next()); + i++; + } + Assertions.assertEquals(10, i); + + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz new file mode 100644 index 0000000000000000000000000000000000000000..6c06bf4e5a5d568aa6c534cc4636796d9938f97e GIT binary patch literal 7412 zcmV44`c0g6Vvm2)J$*9; zQILd$BG?2eTe;eI*ca%jx!CHh+Ka8;CuqOPKFOW~iu$oB*|FrFwjNqPe| zq*``Y6H&he#qs~5p&6x}wEXU+>u-+TGuam=sCmU1!?@QE6MHPb>q~ zJDZ-or$a^p_$O`h7>bL4`aAnIP$;y^3gnay6XugHBMlmjs6P;UrMZXq_xgOq0(F{K zbar>IM~B=WtMf_id!@N+d$iZ%K3BtOALg47J`p`q>qp#6{5XlIPe9F)4-C4<0~&D} zkW-I?LSPc;y!wYA$29Q;IgNn<#N 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zPMSgQpk$3nspD)Q&F3L2n!4}_Xai}CvFtX8Tx#2nE?ym(%HY61tSn5hV5qZ!av1kf zOx;1RJ2;wHq}nQ(g2(>(~xOtR_0x~l(-?w5vZ)*qnG|%O@lQfb Date: Wed, 4 Dec 2024 15:03:59 +0100 Subject: [PATCH 07/15] added zenodoDump to enum of CollectorPlugin --- .../main/java/eu/dnetlib/dhp/collection/CollectorWorker.java | 3 +++ .../java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index f63bfcb48d..4c6d0653eb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -7,6 +7,7 @@ import java.io.IOException; import java.util.Optional; import java.util.concurrent.atomic.AtomicInteger; +import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; @@ -129,6 +130,8 @@ public class CollectorWorker extends ReportingJob { return new Gtr2PublicationsCollectorPlugin(this.clientParams); case osfPreprints: return new OsfPreprintsCollectorPlugin(this.clientParams); + case zenodoDump: + return new CollectZenodoDumpCollectorPlugin(); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional .ofNullable(this.api.getParams().get("other_plugin_type")) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 72e691579b..93e65b6a70 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -11,7 +11,7 @@ public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints; + oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints, zenodoDump; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb From bde59a7c8f49cd964317a9e240dacb3be1eeec01 Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 5 Dec 2024 11:09:30 +0100 Subject: [PATCH 08/15] implementation of the utilities for the inclusion of raids in the graph --- .../java/eu/dnetlib/dhp/common/Constants.java | 4 + .../dnetlib/dhp/actionmanager/Constants.java | 8 + .../raid/GenerateRAiDActionSetJob.java | 190 ++++++++++++++++++ .../raid/model/GenerateRAiDActionSetJob.java | 2 + .../actionmanager/raid/model/RAiDEntity.java | 102 ++++++++++ .../ror/GenerateRorActionSetJob.java | 8 +- .../raid/action_set_parameters.json | 14 ++ .../raid/oozie_app/action_set_parameters.json | 0 .../raid/oozie_app/config-default.xml | 58 ++++++ .../actionmanager/raid/oozie_app/workflow.xml | 55 +++++ .../raid/GenerateRAiDActionSetJobTest.java | 112 +++++++++++ .../dhp/actionmanager/raid/raid_example.json | 6 + 12 files changed, 552 insertions(+), 7 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java index 0477d6399d..b00199ea54 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -10,6 +10,10 @@ public class Constants { public static final Map accessRightsCoarMap = Maps.newHashMap(); public static final Map coarCodeLabelMap = Maps.newHashMap(); + public static final String RAID_NS_PREFIX = "raid________"; + public static final String RAID_DATASOURCE_NAME = "Research Activity Identifier Service (RAiD)"; + public static final String RAID_OPENAIRE_ID = ""; + public static final String ROR_NS_PREFIX = "ror_________"; public static final String ROR_OPENAIRE_ID = "10|openaire____::993a7ae7a863813cf95028b50708e222"; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index 73b4b77cb9..722415c2ed 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -3,6 +3,8 @@ package eu.dnetlib.dhp.actionmanager; import java.util.Optional; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -110,6 +112,12 @@ public class Constants { } + public static Instance getInstance(Qualifier qualifier) { + Instance instance = new Instance(); + instance.setInstancetype(qualifier); + return instance; + } + public static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java new file mode 100644 index 0000000000..8e5e1bdcb0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java @@ -0,0 +1,190 @@ +package eu.dnetlib.dhp.actionmanager.raid; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.Constants; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.DHPUtils; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID; +import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; + +public class GenerateRAiDActionSetJob { + + private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final List RAID_COLLECTED_FROM = listKeyValues( + OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); + + private static final Qualifier RAID_QUALIFIER = qualifier("raid:openaireinference", "raid:openaireinference", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); + + private static final DataInfo RAID_DATA_INFO = dataInfo( + false, OPENAIRE_DATASOURCE_NAME, true, false, RAID_QUALIFIER, "0.92"); + + public static void main(final String[] args) throws Exception { + + final String jsonConfiguration = IOUtils + .toString( + eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + final SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); + processRAiDEntities(spark, inputPath, outputPath); + }); + } + + private static void removeOutputDir(final SparkSession spark, final String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + static void processRAiDEntities(final SparkSession spark, + final String inputPath, + final String outputPath) { + readInputPath(spark, inputPath) + .map(GenerateRAiDActionSetJob::prepareRAiD) + .flatMap(List::iterator) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + + } + + protected static List> prepareRAiD(final RAiDEntity r) { + + final Date now = new Date(); + final OtherResearchProduct orp = new OtherResearchProduct(); + final List> res = new ArrayList<>(); + String raidId = calculateOpenaireId(r.getRaid()); + + orp.setId(raidId); + orp.setCollectedfrom(RAID_COLLECTED_FROM); + orp.setDataInfo(RAID_DATA_INFO); + orp.setResourcetype(RAID_QUALIFIER); + orp.setTitle( + Collections.singletonList( + structuredProperty( + r.getTitle(), + qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE), + RAID_DATA_INFO)) + ); + orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary())); + orp.setAuthor(createAuthors(r.getAuthors())); + orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER))); + orp.setSubject( + r.getSubjects() + .stream() + .map(s -> subject(s, qualifier(DNET_SUBJECT_KEYWORD, DNET_SUBJECT_KEYWORD, DNET_SUBJECT_TYPOLOGIES, DNET_SUBJECT_TYPOLOGIES), RAID_DATA_INFO)) + .collect(Collectors.toList()) + ); + orp.setRelevantdate( + Arrays.asList( + structuredProperty(r.getEndDate(), qualifier("endDate","endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO), + structuredProperty(r.getStartDate(), qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO) + ) + ); + orp.setLastupdatetimestamp(now.getTime()); + orp.setDateofcollection(r.getStartDate()); + + res.add(new AtomicAction<>(OtherResearchProduct.class, orp)); + + for(String resultId: r.getIds()) { + Relation rel1 = OafMapperUtils.getRelation( + raidId, + resultId, + ModelConstants.RESULT_RESULT, + ModelConstants.OUTCOME, + PART, + RAID_COLLECTED_FROM, + RAID_DATA_INFO, + now.getTime(), + null, + null + ); + Relation rel2 = OafMapperUtils.getRelation( + resultId, + raidId, + ModelConstants.RESULT_RESULT, + ModelConstants.OUTCOME, + IS_PART_OF, + RAID_COLLECTED_FROM, + RAID_DATA_INFO, + now.getTime(), + null, + null + ); + res.add(new AtomicAction<>(Relation.class, rel1)); + res.add(new AtomicAction<>(Relation.class, rel2)); + } + + return res; + } + + public static String calculateOpenaireId(final String raid) { + return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid)); + } + + public static List createAuthors(final List author) { + return author.stream().map(s-> { + Author a = new Author(); + a.setFullname(s); + return a; + }).collect(Collectors.toList()); + } + + private static JavaRDD readInputPath( + final SparkSession spark, + final String path) { + + return spark + .read() + .json(path) + .as(Encoders.bean(RAiDEntity.class)) + .toJavaRDD(); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java new file mode 100644 index 0000000000..b0aec71d3f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java @@ -0,0 +1,2 @@ +package eu.dnetlib.dhp.actionmanager.raid.model;public class GenerateRAiDActionSetJob { +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java new file mode 100644 index 0000000000..bd7e28926e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java @@ -0,0 +1,102 @@ +package eu.dnetlib.dhp.actionmanager.raid.model; + +import java.io.Serializable; +import java.util.List; + +public class RAiDEntity implements Serializable { + + String raid; + List authors; + String startDate; + String endDate; + List subjects; + List titles; + List ids; + String title; + String summary; + + public RAiDEntity(){} + public RAiDEntity(String raid, List authors, String startDate, String endDate, List subjects, List titles, List ids, String title, String summary) { + this.raid = raid; + this.authors = authors; + this.startDate = startDate; + this.endDate = endDate; + this.subjects = subjects; + this.titles = titles; + this.ids = ids; + this.title = title; + this.summary = summary; + } + + public String getRaid() { + return raid; + } + + public void setRaid(String raid) { + this.raid = raid; + } + + public List getAuthors() { + return authors; + } + + public void setAuthors(List authors) { + this.authors = authors; + } + + public String getStartDate() { + return startDate; + } + + public void setStartDate(String startDate) { + this.startDate = startDate; + } + + public String getEndDate() { + return endDate; + } + + public void setEndDate(String endDate) { + this.endDate = endDate; + } + + public List getSubjects() { + return subjects; + } + + public void setSubjects(List subjects) { + this.subjects = subjects; + } + + public List getTitles() { + return titles; + } + + public void setTitles(List titles) { + this.titles = titles; + } + + public List getIds() { + return ids; + } + + public void setIds(List ids) { + this.ids = ids; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getSummary() { + return summary; + } + + public void setSummary(String summary) { + this.summary = summary; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index 5f3493d567..ce1973a7f5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -21,6 +21,7 @@ import java.util.Optional; import java.util.Set; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; @@ -44,13 +45,6 @@ import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json new file mode 100644 index 0000000000..2049630d2b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "i", + "paramLongName": "inputPath", + "paramDescription": "the path of the input json", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml new file mode 100644 index 0000000000..a1755f329b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml new file mode 100644 index 0000000000..9b5aa5905e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml @@ -0,0 +1,55 @@ + + + + raidJsonInputPath + the path of the json + + + raidActionSetPath + path where to store the action set + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + yarn + cluster + ProcessRAiDFile + eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --inputPath${raidJsonInputPath} + --outputPath${raidActionSetPath} + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java new file mode 100644 index 0000000000..1f33f45b2b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java @@ -0,0 +1,112 @@ +package eu.dnetlib.dhp.actionmanager.raid; + +import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest; +import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Relation; +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import scala.Tuple2; + +import java.io.File; +import java.nio.file.Paths; +import java.util.Arrays; +import java.util.List; + +import static eu.dnetlib.dhp.actionmanager.Constants.OBJECT_MAPPER; +import static java.nio.file.Files.createTempDirectory; +import static org.junit.jupiter.api.Assertions.assertEquals; + +public class GenerateRAiDActionSetJobTest { + private static String input_path; + private static String output_path; + static SparkSession spark; + + @BeforeEach + void setUp() throws Exception { + + input_path = Paths + .get(GenerateRAiDActionSetJobTest.class.getResource("/eu/dnetlib/dhp/actionmanager/raid/raid_example.json").toURI()) + .toFile() + .getAbsolutePath(); + + output_path = createTempDirectory(GenerateRAiDActionSetJobTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + + SparkConf conf = new SparkConf(); + conf.setAppName(GenerateRAiDActionSetJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", output_path); + conf.set("hive.metastore.warehouse.dir", output_path); + + spark = SparkSession + .builder() + .appName(GenerateRAiDActionSetJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + static void cleanUp() throws Exception { + FileUtils.deleteDirectory(new File(output_path)); + } + + @Test + @Disabled + void testProcessRAiDEntities() { + GenerateRAiDActionSetJob.processRAiDEntities(spark, input_path, output_path + "/test_raid_action_set"); + + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD result = sc + .sequenceFile(output_path + "/test_raid_action_set", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(AtomicAction::getPayload); + + assertEquals(80, result.count()); + } + + @Test + void testPrepareRAiD() { + + List> atomicActions = GenerateRAiDActionSetJob.prepareRAiD(new RAiDEntity( + "-92190526", + Arrays.asList("Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", "Maïeul GRUGET", "Cécile Duchêne"), + "2021-09-10", + "2024-02-16", + Arrays.asList("cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", "General Medicine", "Geography, Planning and Development", "multi-scales", "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", "open source", "drawing", "Constraint", "Multi-scale maps"), + Arrays.asList("Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", "Collection of cartographic disorientation stories", "Anchorwhat dataset", "BasqueRoads: A Benchmark for Road Network Selection", "Progressive river network selection for pan-scalar maps", "BasqueRoads, a dataset to benchmark road selection algorithms", "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", "Empirical approach to advance the generalisation of multi-scale maps", "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", "eye-tracking data from a survey on zooming in a pan-scalar map", "Material of the experiment 'More is Less' from the MapMuxing project", "Cartagen4py, an open source Python library for map generalisation", "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"), + Arrays.asList("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"), + "Exploring Multi-Scale Map Generalization and Design", + "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval." + )); + + OtherResearchProduct orp = (OtherResearchProduct) atomicActions.get(0).getPayload(); + Relation rel = (Relation) atomicActions.get(1).getPayload(); + + assertEquals("Exploring Multi-Scale Map Generalization and Design", orp.getTitle().get(0).getValue()); + assertEquals("50|raid________::759a564ce5cc7360cab030c517c7366b", rel.getSource()); + assertEquals("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", rel.getTarget()); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json new file mode 100644 index 0000000000..7694b605c3 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json @@ -0,0 +1,6 @@ +{"raid": "-9222092103004099540", "authors": ["Department of Archaeology & Museums", "Department of Archaeology and Museums", "Department Of Archaeology & Museums"], "subjects": ["Begamganj", "Raisen", "Bhopal", "Budhni", "Malwa site survey", "सीहोर", "Gauharganj", "बुधनी", "Budni", "Berasia"], "titles": ["Malwa site survey : Raisen District, Begamganj Tahsīl, photographic documentation", "Malwa site survey : Bhopal District, photographic documentation (version 1, TIFF files)", "Malwa site survey : Raisen District, Gauharganj Tahsīl, village finds", "Malwa site survey : Sehore सीहोर District, Budni Tahsīl, photographic documentation (part 1)", "Malwa site survey: Bhopal District, Berasia Tahsīl, photographic documentation (with villages named)", "Malwa site survey : Sehore सीहोर District, Budni Tahsīl, photographic documentation (part 2)", "Malwa site survey : Bhopal District, photographic documentation (version 2, JPEG files)"], "ids": ["50|doi_dedup___::7523d165970830dd857e6cbea4302adf", "50|doi_dedup___::02309ae8a9fae291df321e317f5c5330", "50|doi_dedup___::95347ba2c4264414fab39712ee7fe481", "50|doi_dedup___::970aa708fe667596754fd02a708780f5", "50|doi_dedup___::b7cd9128cc53b1257a4f000347f339b0", "50|doi_dedup___::c7d65da0ecedef4d2c702b9db197d90c", "50|doi_dedup___::addbb67cf5046e340f342ba091bcebfa"], "title": "Documentation of Malwa Region", "summary": "This project involves the documentation of the Malwa region through photographic surveys. The surveys were conducted by the Department of Archaeology and Museums, Madhya Pradesh, and cover various districts and tahsils. The documentation includes photographic records of sites, villages, and other relevant features. The project aims to provide a comprehensive understanding of the region's cultural and historical significance.", "startDate": "2019-03-06", "endDate": "2019-03-08"} +{"raid": "-9221424331076109424", "authors": ["Hutchings, Judy", "Ward, Catherine", "Baban, Adriana", "D��nil��, Ingrid", "Frantz, Inga", "Gardner, Frances", "Lachman, Jamie", "Lachman, Jamie M.", "Foran, Heather", "Heinrichs, Nina", "Murphy, Hugh", "B��ban, Adriana", "Raleva, Marija", "Fang, Xiangming", "Jansen, Elena", "Taut, Diana", "Foran, Heather M.", "T��ut, Diana", "Ward, Catherine L.", "Williams, Margiad", "Lesco, Galina", "Brühl, Antonia"], "subjects": ["3. Good health", "5. Gender equality", "Criminology not elsewhere classified", "1. No poverty", "2. Zero hunger"], "titles": ["sj-docx-1-vaw-10.1177_10778012231188090 - Supplemental material for Co-Occurrence of Intimate Partner Violence Against Mothers and Maltreatment of Their Children With Behavioral Problems in Eastern Europe", "Hunger in vulnerable families in Southeastern Europe: Associations with health and violence", "Prevention of child mental health problems through parenting interventions in Southeastern Europe (RISE): study protocol for a multi-site randomised controlled trial"], "ids": ["50|doi_dedup___::a70015063e5400dae2e097ee10b4a589", "50|doi_dedup___::6e1d12026fcde9087724622ccdeed430", "50|doi_dedup___::5b7bd5d46c5d95e2ef5b36663504a67e"], "title": "Exploring the Impact of Hunger and Violence on Child Health in Southeastern Europe", "summary": "This study aims to investigate the relationship between hunger, violence, and child health in vulnerable families in Southeastern Europe. The research will explore the experiences of families in FYR Macedonia, Republic of Moldova, and Romania, and examine the associations between hunger, maltreatment, and other health indicators. The study will also test the efficacy of a parenting intervention targeting child behavioral problems in alleviating these issues. The findings of this research will contribute to the development of effective interventions to address the complex needs of vulnerable families in the region.", "startDate": "2019-06-04", "endDate": "2023-01-01"} +{"raid": "-9219052635741785098", "authors": ["Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", "Maïeul GRUGET", "Cécile Duchêne"], "subjects": ["cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", "General Medicine", "Geography, Planning and Development", "multi-scales", "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", "open source", "drawing", "Constraint", "Multi-scale maps"], "titles": ["Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", "Collection of cartographic disorientation stories", "Anchorwhat dataset", "BasqueRoads: A Benchmark for Road Network Selection", "Progressive river network selection for pan-scalar maps", "BasqueRoads, a dataset to benchmark road selection algorithms", "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", "Empirical approach to advance the generalisation of multi-scale maps", "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", "eye-tracking data from a survey on zooming in a pan-scalar map", "Material of the experiment \"More is Less\" from the MapMuxing project", "Cartagen4py, an open source Python library for map generalisation", "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"], "ids": ["50|doi_dedup___::6915135e0aa39f913394513f809ae58a", "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"], "title": "Exploring Multi-Scale Map Generalization and Design", "summary": "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval.", "startDate": "2021-09-10", "endDate": "2024-02-16"} +{"raid": "-9216828847055450272", "authors": ["Grey, Alan", "Gorelov, Sergey", "Pall, Szilard", "Merz, Pascal", "Justin A., Lemkul", "Szilárd Páll", "Pasquadibisceglie, Andrea", "Kutzner, Carsten", "Schulz, Roland", "Nabet, Julien", "Abraham, Mark", "Jalalypour, Farzaneh", "Lundborg, Magnus", "Gray, Alan", "Villa, Alessandra", "Berk Hess", "Santuz, Hubert", "Irrgang, M. Eric", "Wingbermuehle, Sebastian", "Lemkul, Justin A.", "Jordan, Joe", "Pellegrino, Michele", "Doijade, Mahesh", "Shvetsov, Alexey", "Hess, Berk", "Behera, Sudarshan", "Andrey Alekseenko", "Shugaeva, Tatiana", "Fleischmann, Stefan", "Bergh, Cathrine", "Morozov, Dmitry", "Adam Hospital", "Briand, Eliane", "Lindahl, Erik", "Brown, Ania", "Marta Lloret Llinares", "Miletic, Vedran", "Alekseenko, Andrey", "Gouaillardet, Gilles", "Fiorin, Giacomo", "Basov, Vladimir"], "subjects": ["webinar"], "titles": ["Introduction to HPC: molecular dynamics simulations with GROMACS: log files", "BioExcel webinar #73: Competency frameworks to support training design and professional development", "Introduction to HPC: molecular dynamics simulations with GROMACS: output files - Devana", "GROMACS 2024.0 Manual", "BioExcel Webinar #71: GROMACS-PMX for accurate estimation of free energy differences", "Introduction to HPC: molecular dynamics simulations with GROMACS: input files", "BioExcel Webinar #68: What's new in GROMACS 2023", "BioExcel Webinar #69: BioBB-Wfs and BioBB-API, integrated web-based platform and programmatic interface for biomolecular simulations workflows using the BioExcel Building Blocks library", "GROMACS 2024-beta Source code"], "ids": ["50|doi_dedup___::8318fbc815ee1943c3269be7567f220b", "50|doi_dedup___::9530e03fb2aac63e82b18a40dc09e32c", "50|doi_dedup___::30174ab31075e76a428ca5b4f4d236b8", "50|doi_________::70b7c6dce09ae6f1361d22913fdf95eb", "50|doi_dedup___::337dd48600618f3c06257edd750d6201", "50|doi_dedup___::d622992ba9077617f37ebd268b3e806d", "50|doi_dedup___::0b0bcc6825d6c052c37882fd5cfc1e8c", "50|doi_dedup___::4b1541a7cee32527c65ace5d1ed57335", "50|doi_dedup___::1379861df59bd755e4fb39b9f95ffbd3"], "title": "Exploring High-Performance Computing and Biomolecular Simulations", "summary": "This project involves exploring high-performance computing (HPC) and biomolecular simulations using GROMACS. The objectives include understanding molecular dynamics simulations, log files, input files, and output files. Additionally, the project aims to explore competency frameworks for professional development, specifically in the field of computational biomolecular research. The tools and techniques used will include GROMACS, BioExcel Building Blocks, and competency frameworks. The expected outcomes include a deeper understanding of HPC and biomolecular simulations, as well as the development of skills in using GROMACS and BioExcel Building Blocks. The project will also contribute to the development of competency frameworks for professional development in the field of computational biomolecular research.", "startDate": "2023-04-25", "endDate": "2024-01-30"} +{"raid": "-9210544816395499758", "authors": ["Bateson, Melissa", "Andrews, Clare", "Verhulst, Simon", "Nettle, Daniel", "Zuidersma, Erica"], "subjects": ["2. Zero hunger"], "titles": ["Exposure to food insecurity increases energy storage and reduces somatic maintenance in European starlings", "Data and code archive for Andrews et al. 'Exposure to food insecurity increases energy storage and reduces somatic maintenance in European starlings'"], "ids": ["50|doi_dedup___::176117239be06189523c253e0ca9c5ec", "50|doi_dedup___::343e0b0ddf0d54763a89a62af1f7a379"], "title": "Investigating the Effects of Food Insecurity on Energy Storage and Somatic Maintenance in European Starlings", "summary": "This study examines the impact of food insecurity on energy storage and somatic maintenance in European starlings. The research involved exposing juvenile starlings to either uninterrupted food availability or a regime of unpredictable food unavailability. The results show that birds exposed to food insecurity stored more energy, but at the expense of somatic maintenance and repair. The study provides insights into the adaptive responses of birds to food scarcity and the trade-offs involved in energy storage and maintenance.", "startDate": "2021-06-28", "endDate": "2021-06-28"} +{"raid": "-9208499171224730388", "authors": ["Maniati, Eleni", "Bakker, Bjorn", "McClelland, Sarah E.", "Shaikh, Nadeem", "De Angelis, Simone", "Johnson, Sarah C.", "Wang, Jun", "Foijer, Floris", "Spierings, Diana C. J.", "Boemo, Michael A.", "Wardenaar, René", "Mazzagatti, Alice"], "subjects": [], "titles": ["Additional file 2 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses", "Additional file 5 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses"], "ids": ["50|doi_dedup___::a1bfeb173971f74a274fab8bdd78a4bc", "50|doi_dedup___::3d6e151aaeb2f7c40a320207fdd80ade"], "title": "Analysis of DNA Copy Number Alterations and Chromosome Scale Losses", "summary": "This study analyzed the effects of replication stress on DNA copy number alterations and chromosome scale losses. The results show distinctive landscapes of these alterations and losses, which were further investigated in additional files. The study provides valuable insights into the mechanisms of replication stress and its impact on genomic stability.", "startDate": "2022-01-01", "endDate": "2022-01-01"} \ No newline at end of file From 6af3fd16b6362c4a9357f44ba779b7822f5b7033 Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 5 Dec 2024 14:39:42 +0100 Subject: [PATCH 09/15] attributes fixes --- .../java/eu/dnetlib/pace/tree/DateRange.java | 90 ++--- .../eu/dnetlib/pace/tree/JsonListMatch.java | 2 +- .../pace/comparators/ComparatorTest.java | 30 +- .../dnetlib/dhp/actionmanager/Constants.java | 4 +- .../raid/GenerateRAiDActionSetJob.java | 309 ++++++++++-------- .../raid/model/GenerateRAiDActionSetJob.java | 5 +- .../actionmanager/raid/model/RAiDEntity.java | 154 ++++----- .../ror/GenerateRorActionSetJob.java | 2 +- .../dhp/sx/bio/pubmed/PMAffiliation.java | 44 +-- .../dnetlib/dhp/sx/bio/pubmed/PMAuthor.java | 1 - .../dhp/sx/bio/pubmed/PMIdentifier.java | 74 ++--- .../raid/oozie_app/action_set_parameters.json | 0 .../actionmanager/raid/oozie_app/workflow.xml | 2 - .../collection/crossref/Crossref2Oaf.scala | 1 - .../dnetlib/dhp/sx/bio/pubmed/PMParser2.scala | 13 +- .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 20 +- .../raid/GenerateRAiDActionSetJobTest.java | 203 +++++++----- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 1 - .../dhp/bulktag/community/ResultTagger.java | 4 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 3 +- .../model/ProvisionModelSupport.java | 15 +- 21 files changed, 546 insertions(+), 431 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java index c913109a48..194677e6eb 100644 --- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java +++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java @@ -1,10 +1,5 @@ -package eu.dnetlib.pace.tree; -import com.wcohen.ss.AbstractStringDistance; -import eu.dnetlib.pace.config.Config; -import eu.dnetlib.pace.tree.support.AbstractStringComparator; -import eu.dnetlib.pace.tree.support.ComparatorClass; -import org.joda.time.DateTime; +package eu.dnetlib.pace.tree; import java.time.DateTimeException; import java.time.LocalDate; @@ -13,55 +8,62 @@ import java.time.format.DateTimeFormatter; import java.util.Locale; import java.util.Map; +import org.joda.time.DateTime; + +import com.wcohen.ss.AbstractStringDistance; + +import eu.dnetlib.pace.config.Config; +import eu.dnetlib.pace.tree.support.AbstractStringComparator; +import eu.dnetlib.pace.tree.support.ComparatorClass; + @ComparatorClass("dateRange") public class DateRange extends AbstractStringComparator { - int YEAR_RANGE; + int YEAR_RANGE; - public DateRange(Map params) { - super(params, new com.wcohen.ss.JaroWinkler()); - YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3")); - } + public DateRange(Map params) { + super(params, new com.wcohen.ss.JaroWinkler()); + YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3")); + } - public DateRange(final double weight) { - super(weight, new com.wcohen.ss.JaroWinkler()); - } + public DateRange(final double weight) { + super(weight, new com.wcohen.ss.JaroWinkler()); + } - protected DateRange(final double weight, final AbstractStringDistance ssalgo) { - super(weight, ssalgo); - } + protected DateRange(final double weight, final AbstractStringDistance ssalgo) { + super(weight, ssalgo); + } - public static boolean isNumeric(String str) { - return str.matches("\\d+"); //match a number with optional '-' and decimal. - } + public static boolean isNumeric(String str) { + return str.matches("\\d+"); // match a number with optional '-' and decimal. + } - @Override - public double distance(final String a, final String b, final Config conf) { - if (a.isEmpty() || b.isEmpty()) { - return -1.0; // return -1 if a field is missing - } + @Override + public double distance(final String a, final String b, final Config conf) { + if (a.isEmpty() || b.isEmpty()) { + return -1.0; // return -1 if a field is missing + } - try { - DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH); - LocalDate d1 = LocalDate.parse(a, formatter); - LocalDate d2 = LocalDate.parse(b, formatter); - Period period = Period.between(d1, d2); + try { + DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH); + LocalDate d1 = LocalDate.parse(a, formatter); + LocalDate d2 = LocalDate.parse(b, formatter); + Period period = Period.between(d1, d2); - return period.getYears() <= YEAR_RANGE? 1.0 : 0.0; - } - catch (DateTimeException e) { - return -1.0; - } + return period.getYears() <= YEAR_RANGE ? 1.0 : 0.0; + } catch (DateTimeException e) { + return -1.0; + } - } + } - @Override - public double getWeight() { - return super.weight; - } + @Override + public double getWeight() { + return super.weight; + } - @Override - protected double normalize(final double d) { - return d; - } + @Override + protected double normalize(final double d) { + return d; + } } diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java index e95d9206e2..d9558df90b 100644 --- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java +++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java @@ -62,7 +62,7 @@ public class JsonListMatch extends AbstractListComparator { Set types = Sets.intersection(typesA, typesB); - if (types.isEmpty()) // if no common type, it is impossible to compare + if (types.isEmpty()) // if no common type, it is impossible to compare return -1; ca = ca.stream().filter(s -> types.contains(s.split("::")[0])).collect(Collectors.toSet()); diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java index 83539de4a8..0abde84bc4 100644 --- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java +++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java @@ -72,14 +72,34 @@ public class ComparatorTest extends AbstractPaceTest { CodeMatch codeMatch = new CodeMatch(params); // names have different codes - assertEquals(0.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ir02", conf)); + assertEquals( + 0.0, + codeMatch + .distance( + "physical oceanography at ctd station june 1998 ev02a", + "physical oceanography at ctd station june 1998 ir02", conf)); // names have same code - assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ev02a", conf)); + assertEquals( + 1.0, + codeMatch + .distance( + "physical oceanography at ctd station june 1998 ev02a", + "physical oceanography at ctd station june 1998 ev02a", conf)); // code is not in both names - assertEquals(-1, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998 ev02a", conf)); - assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998", conf)); + assertEquals( + -1, + codeMatch + .distance( + "physical oceanography at ctd station june 1998", + "physical oceanography at ctd station june 1998 ev02a", conf)); + assertEquals( + 1.0, + codeMatch + .distance( + "physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998", + conf)); } @Test @@ -275,7 +295,7 @@ public class ComparatorTest extends AbstractPaceTest { Arrays .asList( "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"grid\",\"classname\":\"GRID Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"grid_1\"}", - "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"), + "{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"), "authors"); List b = createFieldList( Arrays diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index 722415c2ed..394cc22a35 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -3,8 +3,6 @@ package eu.dnetlib.dhp.actionmanager; import java.util.Optional; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Qualifier; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -15,6 +13,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.Subject; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java index 8e5e1bdcb0..3b24059568 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java @@ -1,15 +1,15 @@ + package eu.dnetlib.dhp.actionmanager.raid; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.Constants; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import eu.dnetlib.dhp.utils.DHPUtils; +import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID; +import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; + +import java.util.*; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; @@ -19,172 +19,191 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.Constants; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; -import java.util.*; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID; -import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; - public class GenerateRAiDActionSetJob { - private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class); + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static final List RAID_COLLECTED_FROM = listKeyValues( - OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); + private static final List RAID_COLLECTED_FROM = listKeyValues( + OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); - private static final Qualifier RAID_QUALIFIER = qualifier("raid:openaireinference", "raid:openaireinference", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); + private static final Qualifier RAID_QUALIFIER = qualifier("0049", "Research Activity Identifier", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE); - private static final DataInfo RAID_DATA_INFO = dataInfo( - false, OPENAIRE_DATASOURCE_NAME, true, false, RAID_QUALIFIER, "0.92"); + private static final Qualifier RAID_INFERENCE_QUALIFIER = qualifier( + "raid:openaireinference", "Inferred by OpenAIRE", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); - public static void main(final String[] args) throws Exception { + private static final DataInfo RAID_DATA_INFO = dataInfo( + false, OPENAIRE_DATASOURCE_NAME, true, false, RAID_INFERENCE_QUALIFIER, "0.92"); - final String jsonConfiguration = IOUtils - .toString( - eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json")); + public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + final String jsonConfiguration = IOUtils + .toString( + eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json")); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - final Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + parser.parseArgument(args); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); - final String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String outputPath = parser.get("outputPath"); - log.info("outputPath {}: ", outputPath); + final String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); - final SparkConf conf = new SparkConf(); + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); - runWithSparkSession(conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, outputPath); - processRAiDEntities(spark, inputPath, outputPath); - }); - } + final SparkConf conf = new SparkConf(); - private static void removeOutputDir(final SparkSession spark, final String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, outputPath); + processRAiDEntities(spark, inputPath, outputPath); + }); + } - static void processRAiDEntities(final SparkSession spark, - final String inputPath, - final String outputPath) { - readInputPath(spark, inputPath) - .map(GenerateRAiDActionSetJob::prepareRAiD) - .flatMap(List::iterator) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + private static void removeOutputDir(final SparkSession spark, final String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } - } + static void processRAiDEntities(final SparkSession spark, + final String inputPath, + final String outputPath) { + readInputPath(spark, inputPath) + .map(GenerateRAiDActionSetJob::prepareRAiD) + .flatMap(List::iterator) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); - protected static List> prepareRAiD(final RAiDEntity r) { + } - final Date now = new Date(); - final OtherResearchProduct orp = new OtherResearchProduct(); - final List> res = new ArrayList<>(); - String raidId = calculateOpenaireId(r.getRaid()); + protected static List> prepareRAiD(final RAiDEntity r) { - orp.setId(raidId); - orp.setCollectedfrom(RAID_COLLECTED_FROM); - orp.setDataInfo(RAID_DATA_INFO); - orp.setResourcetype(RAID_QUALIFIER); - orp.setTitle( - Collections.singletonList( - structuredProperty( - r.getTitle(), - qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE), - RAID_DATA_INFO)) - ); - orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary())); - orp.setAuthor(createAuthors(r.getAuthors())); - orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER))); - orp.setSubject( - r.getSubjects() - .stream() - .map(s -> subject(s, qualifier(DNET_SUBJECT_KEYWORD, DNET_SUBJECT_KEYWORD, DNET_SUBJECT_TYPOLOGIES, DNET_SUBJECT_TYPOLOGIES), RAID_DATA_INFO)) - .collect(Collectors.toList()) - ); - orp.setRelevantdate( - Arrays.asList( - structuredProperty(r.getEndDate(), qualifier("endDate","endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO), - structuredProperty(r.getStartDate(), qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO) - ) - ); - orp.setLastupdatetimestamp(now.getTime()); - orp.setDateofcollection(r.getStartDate()); + final Date now = new Date(); + final OtherResearchProduct orp = new OtherResearchProduct(); + final List> res = new ArrayList<>(); + String raidId = calculateOpenaireId(r.getRaid()); - res.add(new AtomicAction<>(OtherResearchProduct.class, orp)); + orp.setId(raidId); + orp.setCollectedfrom(RAID_COLLECTED_FROM); + orp.setDataInfo(RAID_DATA_INFO); + orp + .setTitle( + Collections + .singletonList( + structuredProperty( + r.getTitle(), + qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE), + RAID_DATA_INFO))); + orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary())); +// orp.setAuthor(createAuthors(r.getAuthors())); + orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER))); + orp + .setSubject( + r + .getSubjects() + .stream() + .map( + s -> subject( + s, + qualifier( + DNET_SUBJECT_KEYWORD, DNET_SUBJECT_KEYWORD, DNET_SUBJECT_TYPOLOGIES, + DNET_SUBJECT_TYPOLOGIES), + RAID_DATA_INFO)) + .collect(Collectors.toList())); + orp + .setRelevantdate( + Arrays + .asList( + structuredProperty( + r.getEndDate(), qualifier("endDate", "endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), + RAID_DATA_INFO), + structuredProperty( + r.getStartDate(), + qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), + RAID_DATA_INFO))); + orp.setLastupdatetimestamp(now.getTime()); + orp.setDateofacceptance(field(r.getStartDate(), RAID_DATA_INFO)); - for(String resultId: r.getIds()) { - Relation rel1 = OafMapperUtils.getRelation( - raidId, - resultId, - ModelConstants.RESULT_RESULT, - ModelConstants.OUTCOME, - PART, - RAID_COLLECTED_FROM, - RAID_DATA_INFO, - now.getTime(), - null, - null - ); - Relation rel2 = OafMapperUtils.getRelation( - resultId, - raidId, - ModelConstants.RESULT_RESULT, - ModelConstants.OUTCOME, - IS_PART_OF, - RAID_COLLECTED_FROM, - RAID_DATA_INFO, - now.getTime(), - null, - null - ); - res.add(new AtomicAction<>(Relation.class, rel1)); - res.add(new AtomicAction<>(Relation.class, rel2)); - } + res.add(new AtomicAction<>(OtherResearchProduct.class, orp)); - return res; - } + for (String resultId : r.getIds()) { + Relation rel1 = OafMapperUtils + .getRelation( + raidId, + resultId, + ModelConstants.RESULT_RESULT, + PART, + HAS_PART, + RAID_COLLECTED_FROM, + RAID_DATA_INFO, + now.getTime(), + null, + null); + Relation rel2 = OafMapperUtils + .getRelation( + resultId, + raidId, + ModelConstants.RESULT_RESULT, + PART, + IS_PART_OF, + RAID_COLLECTED_FROM, + RAID_DATA_INFO, + now.getTime(), + null, + null); + res.add(new AtomicAction<>(Relation.class, rel1)); + res.add(new AtomicAction<>(Relation.class, rel2)); + } - public static String calculateOpenaireId(final String raid) { - return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid)); - } + return res; + } - public static List createAuthors(final List author) { - return author.stream().map(s-> { - Author a = new Author(); - a.setFullname(s); - return a; - }).collect(Collectors.toList()); - } + public static String calculateOpenaireId(final String raid) { + return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid)); + } - private static JavaRDD readInputPath( - final SparkSession spark, - final String path) { + public static List createAuthors(final List author) { + return author.stream().map(s -> { + Author a = new Author(); + a.setFullname(s); + return a; + }).collect(Collectors.toList()); + } - return spark - .read() - .json(path) - .as(Encoders.bean(RAiDEntity.class)) - .toJavaRDD(); + private static JavaRDD readInputPath( + final SparkSession spark, + final String path) { - } + return spark + .read() + .json(path) + .as(Encoders.bean(RAiDEntity.class)) + .toJavaRDD(); + + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java index b0aec71d3f..856b52e181 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java @@ -1,2 +1,5 @@ -package eu.dnetlib.dhp.actionmanager.raid.model;public class GenerateRAiDActionSetJob { + +package eu.dnetlib.dhp.actionmanager.raid.model; + +public class GenerateRAiDActionSetJob { } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java index bd7e28926e..1203b28a76 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.actionmanager.raid.model; import java.io.Serializable; @@ -5,98 +6,101 @@ import java.util.List; public class RAiDEntity implements Serializable { - String raid; - List authors; - String startDate; - String endDate; - List subjects; - List titles; - List ids; - String title; - String summary; + String raid; + List authors; + String startDate; + String endDate; + List subjects; + List titles; + List ids; + String title; + String summary; - public RAiDEntity(){} - public RAiDEntity(String raid, List authors, String startDate, String endDate, List subjects, List titles, List ids, String title, String summary) { - this.raid = raid; - this.authors = authors; - this.startDate = startDate; - this.endDate = endDate; - this.subjects = subjects; - this.titles = titles; - this.ids = ids; - this.title = title; - this.summary = summary; - } + public RAiDEntity() { + } - public String getRaid() { - return raid; - } + public RAiDEntity(String raid, List authors, String startDate, String endDate, List subjects, + List titles, List ids, String title, String summary) { + this.raid = raid; + this.authors = authors; + this.startDate = startDate; + this.endDate = endDate; + this.subjects = subjects; + this.titles = titles; + this.ids = ids; + this.title = title; + this.summary = summary; + } - public void setRaid(String raid) { - this.raid = raid; - } + public String getRaid() { + return raid; + } - public List getAuthors() { - return authors; - } + public void setRaid(String raid) { + this.raid = raid; + } - public void setAuthors(List authors) { - this.authors = authors; - } + public List getAuthors() { + return authors; + } - public String getStartDate() { - return startDate; - } + public void setAuthors(List authors) { + this.authors = authors; + } - public void setStartDate(String startDate) { - this.startDate = startDate; - } + public String getStartDate() { + return startDate; + } - public String getEndDate() { - return endDate; - } + public void setStartDate(String startDate) { + this.startDate = startDate; + } - public void setEndDate(String endDate) { - this.endDate = endDate; - } + public String getEndDate() { + return endDate; + } - public List getSubjects() { - return subjects; - } + public void setEndDate(String endDate) { + this.endDate = endDate; + } - public void setSubjects(List subjects) { - this.subjects = subjects; - } + public List getSubjects() { + return subjects; + } - public List getTitles() { - return titles; - } + public void setSubjects(List subjects) { + this.subjects = subjects; + } - public void setTitles(List titles) { - this.titles = titles; - } + public List getTitles() { + return titles; + } - public List getIds() { - return ids; - } + public void setTitles(List titles) { + this.titles = titles; + } - public void setIds(List ids) { - this.ids = ids; - } + public List getIds() { + return ids; + } - public String getTitle() { - return title; - } + public void setIds(List ids) { + this.ids = ids; + } - public void setTitle(String title) { - this.title = title; - } + public String getTitle() { + return title; + } - public String getSummary() { - return summary; - } + public void setTitle(String title) { + this.title = title; + } - public void setSummary(String summary) { - this.summary = summary; - } + public String getSummary() { + return summary; + } + + public void setSummary(String summary) { + this.summary = summary; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index ce1973a7f5..6e8f48bda2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -21,7 +21,6 @@ import java.util.Optional; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; @@ -45,6 +44,7 @@ import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java index a8dacd1323..5ac1920eaa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.sx.bio.pubmed; /** @@ -7,32 +8,33 @@ package eu.dnetlib.dhp.sx.bio.pubmed; */ public class PMAffiliation { - private String name; + private String name; - private PMIdentifier identifier; + private PMIdentifier identifier; - public PMAffiliation() { + public PMAffiliation() { - } - public PMAffiliation(String name, PMIdentifier identifier) { - this.name = name; - this.identifier = identifier; - } + } - public String getName() { - return name; - } + public PMAffiliation(String name, PMIdentifier identifier) { + this.name = name; + this.identifier = identifier; + } - public void setName(String name) { - this.name = name; - } + public String getName() { + return name; + } - public PMIdentifier getIdentifier() { - return identifier; - } + public void setName(String name) { + this.name = name; + } - public PMAffiliation setIdentifier(PMIdentifier identifier) { - this.identifier = identifier; - return this; - } + public PMIdentifier getIdentifier() { + return identifier; + } + + public PMAffiliation setIdentifier(PMIdentifier identifier) { + this.identifier = identifier; + return this; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java index b0df256634..e023f2e626 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java @@ -97,5 +97,4 @@ public class PMAuthor implements Serializable { this.affiliation = affiliation; } - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java index 0c8c55e40e..6cd17a90c0 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java @@ -1,53 +1,53 @@ + package eu.dnetlib.dhp.sx.bio.pubmed; public class PMIdentifier { - private String pid; - private String type; + private String pid; + private String type; + public PMIdentifier(String pid, String type) { + this.pid = cleanPid(pid); + this.type = type; + } - public PMIdentifier(String pid, String type) { - this.pid = cleanPid(pid); - this.type = type; - } + public PMIdentifier() { - public PMIdentifier() { + } - } + private String cleanPid(String pid) { - private String cleanPid(String pid) { + if (pid == null) { + return null; + } - if (pid == null) { - return null; - } + // clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705 + if (pid.matches("[0-9]{15}[0-9X]")) { + return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4"); + } - // clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705 - if (pid.matches("[0-9]{15}[0-9X]")) { - return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4"); - } + // clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543 + if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) { + return pid.replaceAll("http://orcid.org/", ""); + } + return pid; + } - // clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543 - if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) { - return pid.replaceAll("http://orcid.org/", ""); - } - return pid; - } + public String getPid() { + return pid; + } - public String getPid() { - return pid; - } + public PMIdentifier setPid(String pid) { + this.pid = cleanPid(pid); + return this; + } - public PMIdentifier setPid(String pid) { - this.pid = cleanPid(pid); - return this; - } + public String getType() { + return type; + } - public String getType() { - return type; - } - - public PMIdentifier setType(String type) { - this.type = type; - return this; - } + public PMIdentifier setType(String type) { + this.type = type; + return this; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml index 9b5aa5905e..d3392596fd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml @@ -20,8 +20,6 @@ - - diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala index e4a238c8f3..de68ebb58e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala @@ -673,7 +673,6 @@ case object Crossref2Oaf { val doi = input.getString(0) val rorId = input.getString(1) - val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true) val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala index 2eb4bea65c..bc9a2cf02b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala @@ -82,21 +82,22 @@ class PMParser2 { a.setLastName((author \ "LastName").text) a.setForeName((author \ "ForeName").text) val id = (author \ "Identifier").text - val idType =(author \ "Identifier" \ "@Source").text + val idType = (author \ "Identifier" \ "@Source").text - if(id != null && id.nonEmpty && idType != null && idType.nonEmpty) { + if (id != null && id.nonEmpty && idType != null && idType.nonEmpty) { a.setIdentifier(new PMIdentifier(id, idType)) } - val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text - val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text + val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text - if(affiliation != null && affiliation.nonEmpty) { + if (affiliation != null && affiliation.nonEmpty) { val aff = new PMAffiliation() aff.setName(affiliation) - if(affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty) { + if ( + affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty + ) { aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType)) } a.setAffiliation(aff) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 5e14c731a6..281ca0e07d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -294,11 +294,23 @@ object PubMedToOaf { author.setName(a.getForeName) author.setSurname(a.getLastName) author.setFullname(a.getFullName) - if(a.getIdentifier != null) { - author.setPid(List(OafMapperUtils.structuredProperty(a.getIdentifier.getPid, - OafMapperUtils.qualifier(a.getIdentifier.getType,a.getIdentifier.getType,ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES), dataInfo)).asJava) + if (a.getIdentifier != null) { + author.setPid( + List( + OafMapperUtils.structuredProperty( + a.getIdentifier.getPid, + OafMapperUtils.qualifier( + a.getIdentifier.getType, + a.getIdentifier.getType, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES + ), + dataInfo + ) + ).asJava + ) } - if (a.getAffiliation!= null) + if (a.getAffiliation != null) author.setRawAffiliationString(List(a.getAffiliation.getName).asJava) author.setRank(index + 1) author diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java index 1f33f45b2b..9417822af8 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java @@ -1,11 +1,16 @@ + package eu.dnetlib.dhp.actionmanager.raid; -import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest; -import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Relation; +import static java.nio.file.Files.createTempDirectory; + +import static eu.dnetlib.dhp.actionmanager.Constants.OBJECT_MAPPER; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.File; +import java.nio.file.Paths; +import java.util.Arrays; +import java.util.List; + import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat; @@ -20,93 +25,141 @@ import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest; +import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; -import java.io.File; -import java.nio.file.Paths; -import java.util.Arrays; -import java.util.List; - -import static eu.dnetlib.dhp.actionmanager.Constants.OBJECT_MAPPER; -import static java.nio.file.Files.createTempDirectory; -import static org.junit.jupiter.api.Assertions.assertEquals; - public class GenerateRAiDActionSetJobTest { - private static String input_path; - private static String output_path; - static SparkSession spark; + private static String input_path; + private static String output_path; + static SparkSession spark; - @BeforeEach - void setUp() throws Exception { + @BeforeEach + void setUp() throws Exception { - input_path = Paths - .get(GenerateRAiDActionSetJobTest.class.getResource("/eu/dnetlib/dhp/actionmanager/raid/raid_example.json").toURI()) - .toFile() - .getAbsolutePath(); + input_path = Paths + .get( + GenerateRAiDActionSetJobTest.class + .getResource("/eu/dnetlib/dhp/actionmanager/raid/raid_example.json") + .toURI()) + .toFile() + .getAbsolutePath(); - output_path = createTempDirectory(GenerateRAiDActionSetJobTest.class.getSimpleName() + "-") - .toAbsolutePath() - .toString(); + output_path = createTempDirectory(GenerateRAiDActionSetJobTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); - SparkConf conf = new SparkConf(); - conf.setAppName(GenerateRAiDActionSetJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(GenerateRAiDActionSetJobTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", output_path); - conf.set("hive.metastore.warehouse.dir", output_path); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", output_path); + conf.set("hive.metastore.warehouse.dir", output_path); - spark = SparkSession - .builder() - .appName(GenerateRAiDActionSetJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(GenerateRAiDActionSetJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - static void cleanUp() throws Exception { - FileUtils.deleteDirectory(new File(output_path)); - } + @AfterAll + static void cleanUp() throws Exception { + FileUtils.deleteDirectory(new File(output_path)); + } - @Test - @Disabled - void testProcessRAiDEntities() { - GenerateRAiDActionSetJob.processRAiDEntities(spark, input_path, output_path + "/test_raid_action_set"); + @Test + @Disabled + void testProcessRAiDEntities() { + GenerateRAiDActionSetJob.processRAiDEntities(spark, input_path, output_path + "/test_raid_action_set"); - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD result = sc - .sequenceFile(output_path + "/test_raid_action_set", Text.class, Text.class) - .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(AtomicAction::getPayload); + JavaRDD result = sc + .sequenceFile(output_path + "/test_raid_action_set", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(AtomicAction::getPayload); - assertEquals(80, result.count()); - } + assertEquals(80, result.count()); + } - @Test - void testPrepareRAiD() { + @Test + void testPrepareRAiD() { - List> atomicActions = GenerateRAiDActionSetJob.prepareRAiD(new RAiDEntity( - "-92190526", - Arrays.asList("Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", "Maïeul GRUGET", "Cécile Duchêne"), - "2021-09-10", - "2024-02-16", - Arrays.asList("cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", "General Medicine", "Geography, Planning and Development", "multi-scales", "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", "open source", "drawing", "Constraint", "Multi-scale maps"), - Arrays.asList("Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", "Collection of cartographic disorientation stories", "Anchorwhat dataset", "BasqueRoads: A Benchmark for Road Network Selection", "Progressive river network selection for pan-scalar maps", "BasqueRoads, a dataset to benchmark road selection algorithms", "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", "Empirical approach to advance the generalisation of multi-scale maps", "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", "eye-tracking data from a survey on zooming in a pan-scalar map", "Material of the experiment 'More is Less' from the MapMuxing project", "Cartagen4py, an open source Python library for map generalisation", "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"), - Arrays.asList("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"), - "Exploring Multi-Scale Map Generalization and Design", - "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval." - )); + List> atomicActions = GenerateRAiDActionSetJob + .prepareRAiD( + new RAiDEntity( + "-92190526", + Arrays + .asList( + "Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", + "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", + "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", + "Maïeul GRUGET", "Cécile Duchêne"), + "2021-09-10", + "2024-02-16", + Arrays + .asList( + "cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", + "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", + "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", + "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", + "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", + "General Medicine", "Geography, Planning and Development", "multi-scales", + "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", + "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", + "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", + "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", + "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", + "open source", "drawing", "Constraint", "Multi-scale maps"), + Arrays + .asList( + "Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", + "Collection of cartographic disorientation stories", "Anchorwhat dataset", + "BasqueRoads: A Benchmark for Road Network Selection", + "Progressive river network selection for pan-scalar maps", + "BasqueRoads, a dataset to benchmark road selection algorithms", + "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", + "Empirical approach to advance the generalisation of multi-scale maps", + "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", + "eye-tracking data from a survey on zooming in a pan-scalar map", + "Material of the experiment 'More is Less' from the MapMuxing project", + "Cartagen4py, an open source Python library for map generalisation", + "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"), + Arrays + .asList( + "50|doi_dedup___::6915135e0aa39f913394513f809ae58a", + "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", + "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", + "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", + "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", + "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", + "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", + "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", + "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", + "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", + "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", + "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", + "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", + "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"), + "Exploring Multi-Scale Map Generalization and Design", + "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval.")); - OtherResearchProduct orp = (OtherResearchProduct) atomicActions.get(0).getPayload(); - Relation rel = (Relation) atomicActions.get(1).getPayload(); + OtherResearchProduct orp = (OtherResearchProduct) atomicActions.get(0).getPayload(); + Relation rel = (Relation) atomicActions.get(1).getPayload(); - assertEquals("Exploring Multi-Scale Map Generalization and Design", orp.getTitle().get(0).getValue()); - assertEquals("50|raid________::759a564ce5cc7360cab030c517c7366b", rel.getSource()); - assertEquals("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", rel.getTarget()); + assertEquals("Exploring Multi-Scale Map Generalization and Design", orp.getTitle().get(0).getValue()); + assertEquals("50|raid________::759a564ce5cc7360cab030c517c7366b", rel.getSource()); + assertEquals("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", rel.getTarget()); - } + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index 4a926df015..cb7826dbff 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -63,7 +63,6 @@ class BioScholixTest extends AbstractVocabularyTest { "0000000333457333", "0000000335964515", "0000000302921949", - "http://orcid.org/0000-0001-8567-3543", "http://orcid.org/0000-0001-7868-8528", "0000-0001-9189-1440", diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 64cbd70bac..0d6c816278 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -130,7 +130,7 @@ public class ResultTagger implements Serializable { // log.info("Remove constraints for " + communityId); if (conf.getRemoveConstraintsMap().keySet().contains(communityId) && conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && - !conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() && + !conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() && conf .getRemoveConstraintsMap() .get(communityId) @@ -228,7 +228,7 @@ public class ResultTagger implements Serializable { .forEach(communityId -> { if (!removeCommunities.contains(communityId) && conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null && - !conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() && + !conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() && conf .getSelectionConstraintsMap() .get(communityId) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index ea9503d179..e1710db547 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -915,7 +915,8 @@ class MappersTest { @Test void testODFRecord_guidelines4() throws IOException { - final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml"))); + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); final Publication p = (Publication) list.get(0); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java index 0da0f6955c..2c977a390b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java @@ -5,7 +5,6 @@ import java.io.StringReader; import java.util.*; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.solr.PersonTopic; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -40,6 +39,7 @@ import eu.dnetlib.dhp.schema.solr.OpenAccessColor; import eu.dnetlib.dhp.schema.solr.OpenAccessRoute; import eu.dnetlib.dhp.schema.solr.Organization; import eu.dnetlib.dhp.schema.solr.Person; +import eu.dnetlib.dhp.schema.solr.PersonTopic; import eu.dnetlib.dhp.schema.solr.Pid; import eu.dnetlib.dhp.schema.solr.Project; import eu.dnetlib.dhp.schema.solr.Result; @@ -216,11 +216,14 @@ public class ProvisionModelSupport { } private static List mapPersonTopics(List subjects) { - return Optional.ofNullable(subjects) - .map(ss -> ss.stream() - .map(ProvisionModelSupport::mapPersonTopic) - .collect(Collectors.toList())) - .orElse(null); + return Optional + .ofNullable(subjects) + .map( + ss -> ss + .stream() + .map(ProvisionModelSupport::mapPersonTopic) + .collect(Collectors.toList())) + .orElse(null); } private static PersonTopic mapPersonTopic(eu.dnetlib.dhp.schema.oaf.PersonTopic pt) { From 1c144a4dcb951319ed88a7cac4825837c5385316 Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 6 Dec 2024 09:18:10 +0100 Subject: [PATCH 10/15] minor change --- .../dhp/actionmanager/raid/GenerateRAiDActionSetJob.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java index 3b24059568..c82934cdb3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java @@ -43,7 +43,8 @@ public class GenerateRAiDActionSetJob { private static final List RAID_COLLECTED_FROM = listKeyValues( OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); - private static final Qualifier RAID_QUALIFIER = qualifier("0049", "Research Activity Identifier", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE); + private static final Qualifier RAID_QUALIFIER = qualifier( + "0049", "Research Activity Identifier", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE); private static final Qualifier RAID_INFERENCE_QUALIFIER = qualifier( "raid:openaireinference", "Inferred by OpenAIRE", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS); From dade7d5bb86d4030fc2b69f3a26940e055e216eb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 6 Dec 2024 10:02:07 +0100 Subject: [PATCH 11/15] minor changes --- .../java/eu/dnetlib/dhp/common/Constants.java | 5 ++-- .../raid/GenerateRAiDActionSetJob.java | 27 +++++++------------ 2 files changed, 13 insertions(+), 19 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java index b00199ea54..6a4bb34d3f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java @@ -11,8 +11,9 @@ public class Constants { public static final Map coarCodeLabelMap = Maps.newHashMap(); public static final String RAID_NS_PREFIX = "raid________"; - public static final String RAID_DATASOURCE_NAME = "Research Activity Identifier Service (RAiD)"; - public static final String RAID_OPENAIRE_ID = ""; + + public static final String END_DATE = "endDate"; + public static final String START_DATE = "startDate"; public static final String ROR_NS_PREFIX = "ror_________"; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java index c82934cdb3..e67e7171fb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.actionmanager.raid; import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID; import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME; +import static eu.dnetlib.dhp.common.Constants.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; @@ -24,7 +25,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; @@ -120,8 +120,10 @@ public class GenerateRAiDActionSetJob { qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE), RAID_DATA_INFO))); orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary())); -// orp.setAuthor(createAuthors(r.getAuthors())); - orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER))); + + Instance instance = new Instance(); + instance.setInstancetype(RAID_QUALIFIER); + orp.setInstance(Collections.singletonList(instance)); orp .setSubject( r @@ -140,11 +142,11 @@ public class GenerateRAiDActionSetJob { Arrays .asList( structuredProperty( - r.getEndDate(), qualifier("endDate", "endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), + r.getEndDate(), qualifier(END_DATE, END_DATE, DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO), structuredProperty( r.getStartDate(), - qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), + qualifier(START_DATE, START_DATE, DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO))); orp.setLastupdatetimestamp(now.getTime()); orp.setDateofacceptance(field(r.getStartDate(), RAID_DATA_INFO)); @@ -159,11 +161,7 @@ public class GenerateRAiDActionSetJob { ModelConstants.RESULT_RESULT, PART, HAS_PART, - RAID_COLLECTED_FROM, - RAID_DATA_INFO, - now.getTime(), - null, - null); + orp); Relation rel2 = OafMapperUtils .getRelation( resultId, @@ -171,11 +169,7 @@ public class GenerateRAiDActionSetJob { ModelConstants.RESULT_RESULT, PART, IS_PART_OF, - RAID_COLLECTED_FROM, - RAID_DATA_INFO, - now.getTime(), - null, - null); + orp); res.add(new AtomicAction<>(Relation.class, rel1)); res.add(new AtomicAction<>(Relation.class, rel2)); } @@ -184,7 +178,7 @@ public class GenerateRAiDActionSetJob { } public static String calculateOpenaireId(final String raid) { - return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid)); + return String.format("50|%s::%s", RAID_NS_PREFIX, DHPUtils.md5(raid)); } public static List createAuthors(final List author) { @@ -204,7 +198,6 @@ public class GenerateRAiDActionSetJob { .json(path) .as(Encoders.bean(RAiDEntity.class)) .toJavaRDD(); - } } From 8a5ba8df45d6fb1b570853307fb99f465d0667f5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 6 Dec 2024 10:03:11 +0100 Subject: [PATCH 12/15] minor changes --- .../main/java/eu/dnetlib/dhp/actionmanager/Constants.java | 6 ------ 1 file changed, 6 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index 394cc22a35..d7ad7fcb95 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -112,12 +112,6 @@ public class Constants { } - public static Instance getInstance(Qualifier qualifier) { - Instance instance = new Instance(); - instance.setInstancetype(qualifier); - return instance; - } - public static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } From ee84db7a6a5ff1e271f5d6a0cfdfcc07e1a59ac9 Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Fri, 6 Dec 2024 12:20:13 +0100 Subject: [PATCH 13/15] [communityfromsemrelpropagation] added filtering to remove the deletedbyinference and invisible results --- .../PrepareResultCommunitySetStep1.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index 5af2bf4812..764390442d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -70,7 +70,7 @@ public class PrepareResultCommunitySetStep1 { private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context \n" + " from result " + " lateral view explode (context) c as co " + - " where datainfo.deletedbyinference = false AND lower(co.id) IN %s" + + " where lower(co.id) IN %s" + " group by id"; private static final String RESULT_PATENT = "select id " + @@ -160,7 +160,8 @@ public class PrepareResultCommunitySetStep1 { Dataset relation = readPath(spark, inputRelationPath, Relation.class); relation.createOrReplaceTempView("relation"); - Dataset result = readPath(spark, inputResultPath, resultClazz); + Dataset result = readPath(spark, inputResultPath, resultClazz) + .where("datainfo.deletedbyinference != true AND datainfo.invisible != true"); result.createOrReplaceTempView("result"); final String outputResultPath = outputPath + "/" + resultType; From 666155bafaa04db7153c98d91b911d88e9cb2f01 Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Fri, 6 Dec 2024 12:26:41 +0100 Subject: [PATCH 14/15] [communityfromsemrelpropagation] changed resource to have deletedbyinference = false. --- .../graph/publication/part-00000.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json index 7957bcfd50..ae9083c655 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json @@ -7,7 +7,7 @@ {"author":[{"fullname":"Turkia, Heidi","name":"Heidi","pid":[],"rank":1,"surname":"Turkia"},{"fullname":"Sirén, Heli","name":"Heli","pid":[],"rank":2,"surname":"Sirén"},{"fullname":"Penttilä, Merja","name":"Merja","pid":[],"rank":3,"surname":"Penttilä"},{"fullname":"Pitkänen, Juha Pekka","name":"Juha Pekka","pid":[],"rank":4,"surname":"Pitkänen"}],"bestaccessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"}],"context":[],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2013-02-22"},"dateofcollection":"2022-02-28T12:29:51.291Z","dateoftransformation":"2022-02-28T16:19:35.201Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"

Hydrolysates of lignocellulosic biomass, used as substrates for the sustainable production of fuels and chemicals often contain high amounts of phenolic compounds inhibiting the production microbiota. Quantification of these inhibitor compounds may help to understand possible difficulties in bioprocessing and further the development of more efficient, robust and tolerable processes. A separation method based on capillary electrophoresis with UV detection was developed for the simultaneous quantification of 10 phenolic compounds that may have inhibitor properties. Intraday relative standard deviations were less than 0.7% for migration times and between 2.6% and 6.4% for peak areas. Interday relative standard deviations were less than 3.0% for migration times and between 5.0% and 7.2% for peak areas. The method was applied to demonstrate that Saccharomyces cerevisiae was able to decrease the concentrations of vanillin, coniferyl aldehyde, syringaldehyde, acetoguaiacone and cinnamic acid during the cultivation, whereas the concentrations of phenols increased.

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Results include drying rates for 1.5 mm thick birch veneers as well as 1.5 mm and 2.6 mm thick spruce veneers of both heartwood and sapwood. Based on the test results, material parameter values for a simplified drying model are assessed. The model is based on the use of an effective diffusion coefficient and an effective surface emission coefficient, which values are calibrated to fit to the experimental results. 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, R , Vanttaja , I , Haapamäki , P & Kujanpää , V 1994 , ' Liimauksen ja puristusliittämisen yhdistämisellä lisää lujuutta, jäykkyyttä ja tiiveyttä ' , Ohutlevyuutiset , no. 2 , pp. 17-19 ."}],"subject":[],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Liimauksen ja puristusliittämisen yhdistämisellä lisää lujuutta, jäykkyyttä ja tiiveyttä"}]} \ No newline at end of file From e4b814b3f1bdb3ab52a439aff82aa56359a80cb7 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 6 Dec 2024 13:58:39 +0100 Subject: [PATCH 15/15] code formatting --- .../dhp/collection/CollectorWorker.java | 2 +- .../collection/crossref/Crossref2Oaf.scala | 13 ++-- .../crossref/CrossrefMappingTest.scala | 18 +++-- .../PrepareResultCommunitySetStep1.java | 76 ++++++++++--------- .../PrepareResultCommunitySetStep2.java | 2 +- .../ResultToCommunityJobTest.java | 70 ++++++++--------- 6 files changed, 97 insertions(+), 84 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index 4c6d0653eb..67966d523a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -7,7 +7,6 @@ import java.io.IOException; import java.util.Optional; import java.util.concurrent.atomic.AtomicInteger; -import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; @@ -29,6 +28,7 @@ import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.osf.OsfPreprintsCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; import eu.dnetlib.dhp.common.collection.HttpClientParams; diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala index c72b366a0f..ea2177497a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala @@ -503,7 +503,6 @@ case object Crossref2Oaf { ) } - if (doi.startsWith("10.3410") || doi.startsWith("10.12703")) instance.setHostedby( OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true), "H1Connect") @@ -556,14 +555,18 @@ case object Crossref2Oaf { result } - - def generateIdentifier(oaf: Result, doi: String): String = { val id = DHPUtils.md5(doi.toLowerCase) s"50|doiboost____|$id" } - private def generateAuthor(given: String, family: String, orcid: String, index: Int, affiliation: Option[List[mappingAffiliation]]): Author = { + private def generateAuthor( + given: String, + family: String, + orcid: String, + index: Int, + affiliation: Option[List[mappingAffiliation]] + ): Author = { val a = new Author a.setName(given) a.setSurname(family) @@ -700,7 +703,6 @@ case object Crossref2Oaf { if (objectType == null) return resultList - // If the item has a relations is-review-of, then we force it to a peer-review val is_review = json \ "relation" \ "is-review-of" \ "id" var force_to_review = false @@ -713,7 +715,6 @@ case object Crossref2Oaf { if (typology == null) return List() - val result = generateItemFromType(typology._2) if (result == null) return List() diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala index 12ca14ba14..ebe247d8aa 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala @@ -28,17 +28,21 @@ class CrossrefMappingTest extends AbstractVocabularyTest { val input = IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8") - Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => { - Assertions.assertNotNull(record) - }) + Crossref2Oaf + .convert(input, vocabularies, TransformationType.All) + .foreach(record => { + Assertions.assertNotNull(record) + }) } - @Test def mappingAffiliation(): Unit = { val input = - IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8") + IOUtils.toString( + getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), + "utf-8" + ) val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult) data.foreach(record => { Assertions.assertNotNull(record) @@ -46,10 +50,10 @@ class CrossrefMappingTest extends AbstractVocabularyTest { val publication = record.asInstanceOf[Publication] publication.getAuthor.asScala.foreach(author => { Assertions.assertNotNull(author.getRawAffiliationString) - Assertions.assertTrue(author.getRawAffiliationString.size()>0) + Assertions.assertTrue(author.getRawAffiliationString.size() > 0) - }) }) + }) println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head)) } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index 764390442d..ecb7cc8272 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -1,16 +1,16 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; +import static java.lang.String.join; + import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; -import static java.lang.String.join; import java.io.IOException; import java.util.Arrays; import java.util.Collections; import java.util.List; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.sql.*; @@ -22,6 +22,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.api.Utils; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.utils.ISLookupClientFactory; @@ -37,8 +38,7 @@ public class PrepareResultCommunitySetStep1 { * relation */ // TODO - private static final String RESULT_CONTEXT_QUERY_TEMPLATE = - "select target resultId, community_context " + private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context " + "from (select id, collect_set(co.id) community_context " + " from result " + " lateral view explode (context) c as co " @@ -60,26 +60,26 @@ public class PrepareResultCommunitySetStep1 { + "where length(co) > 0 " + "group by resultId"; - private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = - "select target as resultId, community_context " + - "from resultWithContext rwc " + - "join relatedToRelations r " + - "join patents p " + - "on rwc.id = r.source and r.target = p.id"; + private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target as resultId, community_context " + + + "from resultWithContext rwc " + + "join relatedToRelations r " + + "join patents p " + + "on rwc.id = r.source and r.target = p.id"; private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context \n" + - " from result " + - " lateral view explode (context) c as co " + - " where lower(co.id) IN %s" + - " group by id"; + " from result " + + " lateral view explode (context) c as co " + + " where lower(co.id) IN %s" + + " group by id"; private static final String RESULT_PATENT = "select id " + - " from result " + - " where array_contains(instance.instancetype.classname, 'Patent')"; + " from result " + + " where array_contains(instance.instancetype.classname, 'Patent')"; private static final String IS_RELATED_TO_RELATIONS = "select source, target " + - " from relation " + - " where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false"; + " from relation " + + " where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false"; public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -107,17 +107,25 @@ public class PrepareResultCommunitySetStep1 { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final String allowedsemrel ="(" + join(",", - Arrays.asList(parser.get("allowedsemrels").split(";")).stream().map(value -> "'" + value.toLowerCase() + "'") - .toArray(String[]::new)) + ")"; + final String allowedsemrel = "(" + join( + ",", + Arrays + .asList(parser.get("allowedsemrels").split(";")) + .stream() + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)) + + ")"; log.info("allowedSemRel: {}", allowedsemrel); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}", baseURL); - final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream() + final String communityIdList = "(" + join( + ",", getCommunityList(baseURL) + .stream() .map(value -> "'" + value.toLowerCase() + "'") - .toArray(String[]::new)) + ")"; + .toArray(String[]::new)) + + ")"; final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase(); log.info("resultType: {}", resultType); @@ -161,18 +169,17 @@ public class PrepareResultCommunitySetStep1 { relation.createOrReplaceTempView("relation"); Dataset result = readPath(spark, inputResultPath, resultClazz) - .where("datainfo.deletedbyinference != true AND datainfo.invisible != true"); + .where("datainfo.deletedbyinference != true AND datainfo.invisible != true"); result.createOrReplaceTempView("result"); final String outputResultPath = outputPath + "/" + resultType; log.info("writing output results to: {}", outputResultPath); - String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - "AND lower(co.id) IN " + communityIdList, - "AND lower(relClass) IN " + allowedsemrel); + "AND lower(co.id) IN " + communityIdList, + "AND lower(relClass) IN " + allowedsemrel); Dataset result_context = spark.sql(resultContextQuery); Dataset rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList)); @@ -183,18 +190,17 @@ public class PrepareResultCommunitySetStep1 { patents.createOrReplaceTempView("patents"); relatedToRelations.createOrReplaceTempView("relatedTorelations"); - - result_context = result_context.unionAll( spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO)); + result_context = result_context.unionAll(spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO)); result_context.createOrReplaceTempView("result_context"); spark - .sql(RESULT_COMMUNITY_LIST_QUERY) - .as(Encoders.bean(ResultCommunityList.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .json(outputResultPath); + .sql(RESULT_COMMUNITY_LIST_QUERY) + .as(Encoders.bean(ResultCommunityList.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Append) + .json(outputResultPath); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java index 9bebc36e58..9801b1bf6e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java @@ -77,7 +77,7 @@ public class PrepareResultCommunitySetStep2 { if (b == null) { return a; } - Set community_set = new HashSet<>(a.getCommunityList()); + Set community_set = new HashSet<>(a.getCommunityList()); community_set.addAll(b.getCommunityList()); a.setCommunityList(new ArrayList<>(community_set)); return a; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index c1fcff4d99..2b52c91de4 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java @@ -10,7 +10,6 @@ import java.util.ArrayList; import java.util.List; import java.util.stream.Collectors; -import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -27,6 +26,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; import eu.dnetlib.dhp.schema.oaf.Dataset; import scala.collection.Seq; @@ -279,53 +279,55 @@ public class ResultToCommunityJobTest { @Test public void prepareStep1Test() throws Exception { /* - - - final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) - .map(value -> "'" + value.toLowerCase() + "'") - .toArray(String[]::new)); - - log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); - - final String baseURL = parser.get("baseURL"); - log.info("baseURL: {}", baseURL); + * final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) .map(value -> + * "'" + value.toLowerCase() + "'") .toArray(String[]::new)); log.info("allowedSemRel: {}", new + * Gson().toJson(allowedsemrel)); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}", + * baseURL); */ PrepareResultCommunitySetStep1 - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", getClass() - .getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph") - .getPath(), - "-hive_metastore_uris", "", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/preparedInfo", - "-allowedsemrels","issupplementto;issupplementedby", - "-baseURL","https://dev-openaire.d4science.org/openaire/community/" - }); + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass() + .getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph") + .getPath(), + "-hive_metastore_uris", "", + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", workingDir.toString() + "/preparedInfo", + "-allowedsemrels", "issupplementto;issupplementedby", + "-baseURL", "https://dev-openaire.d4science.org/openaire/community/" + }); - - org.apache.spark.sql.Dataset resultCommunityList = spark.read().schema(Encoders.bean(ResultCommunityList.class).schema()) - .json(workingDir.toString() + "/preparedInfo/publication") - .as(Encoders.bean(ResultCommunityList.class)); + org.apache.spark.sql.Dataset resultCommunityList = spark + .read() + .schema(Encoders.bean(ResultCommunityList.class).schema()) + .json(workingDir.toString() + "/preparedInfo/publication") + .as(Encoders.bean(ResultCommunityList.class)); Assertions.assertEquals(2, resultCommunityList.count()); - Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count()); - Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count()); + Assertions + .assertEquals( + 1, + resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count()); + Assertions + .assertEquals( + 1, + resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count()); ArrayList communities = resultCommunityList - .filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'") - .first().getCommunityList(); + .filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'") + .first() + .getCommunityList(); Assertions.assertEquals(2, communities.size()); Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid))); Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid))); communities = resultCommunityList - .filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'") - .first().getCommunityList(); + .filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'") + .first() + .getCommunityList(); Assertions.assertEquals(1, communities.size()); Assertions.assertEquals("dh-ch", communities.get(0)); } - }